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jonaspatronjp / GWIZ-Rscript

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linear regression / logistic regression? #1

Open janet-Chang opened 2 years ago

janet-Chang commented 2 years ago

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R")
genereteBatch(folderPath, folderOut, files[[j]])
studies <- dir(paste(filename, "/out", sep=""))
## only csv files
studies <- studies[grep(".csv", studies)]
source("./modeling/_modelingFunctions_lda.R")
batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L,
          outerRep = 2L)#, classifier = "classif.logreg")
studyname = substring(files[[j]], 1, 13)
aucout[j,] <- c(studyname, aucanalysis)
colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1] "=================================================================================" [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study: Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk" [1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

jonaspatronjp commented 2 years ago

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1] "=================================================================================" [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study: Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk" [1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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janet-Chang commented 2 years ago

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1] "=================================================================================" [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study: Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk" [1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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jonaspatronjp commented 2 years ago

Could you send me the csv data files you are working with? (i.e. Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv and Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv)

I just freshly pulled the code from github and was able to run it on my computer, so my first guess is that maybe something messed up the datasets on your computer?

Thank you in advance,

Jonas

On Mon, Jul 19, 2021 at 3:57 PM janet Chang @.***> wrote:

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1]

"=================================================================================" [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study:

Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk" [1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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janet-Chang commented 2 years ago

Thanks a lot, Jonas:

I got all this from a professor, he is using your code on his population project, I am supporting his research at the computing center. Originally, he tried to run on his PC, and got the similar error. For convenience, I moved everything to the HPC cluster.

I used conda to install R version 4.1.0, pull the code from your github page directly on the cluster. The Data folder looked like this:

(Renv4II) @. Data]$ ls Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv (Renv4II) @. Data]$

If I open the file, they look like as attached on the cluster, typical csv file. I am also attaching those two csv files downloaded from the cluster.

I tried to change them into tab delimited file, didn't work. I also checked the other functions briefly, it is logistics regression, which shall accept non-numerical values. But the error message was complaining about linear regression lm.fit ?

Thanks again for all your help.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Tuesday, July 20, 2021 1:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Could you send me the csv data files you are working with? (i.e. Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv and Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv)

I just freshly pulled the code from github and was able to run it on my computer, so my first guess is that maybe something messed up the datasets on your computer?

Thank you in advance,

Jonas

On Mon, Jul 19, 2021 at 3:57 PM janet Chang @.***> wrote:

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1]

"=================================================================================" [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study:

Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk" [1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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jonaspatronjp commented 2 years ago

Hi Janet,

I tried running the GWIZ code using R v 4.1.0 and also got an error (albeit a slightly different one). Try running the code using R v 3. I am not entirely sure why, but I believe GWIZ is only compatible with R v 3. It should be possible to download multiple versions of R on your machine and switch between them so that you do not lose all of the packages you already have installed under your R v 4.

Let me know if that fixes anything!

All best,

Jonas

On Tue, Jul 20, 2021 at 11:59 AM janet Chang @.***> wrote:

Thanks a lot, Jonas:

I got all this from a professor, he is using your code on his population project, I am supporting his research at the computing center. Originally, he tried to run on his PC, and got the similar error. For convenience, I moved everything to the HPC cluster.

I used conda to install R version 4.1.0, pull the code from your github page directly on the cluster. The Data folder looked like this:

(Renv4II) @. Data]$ ls Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv (Renv4II) @. Data]$

If I open the file, they look like as attached on the cluster, typical csv file. I am also attaching those two csv files downloaded from the cluster.

I tried to change them into tab delimited file, didn't work. I also checked the other functions briefly, it is logistics regression, which shall accept non-numerical values. But the error message was complaining about linear regression lm.fit ?

Thanks again for all your help.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Tuesday, July 20, 2021 1:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Could you send me the csv data files you are working with? (i.e. Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv and Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv)

I just freshly pulled the code from github and was able to run it on my computer, so my first guess is that maybe something messed up the datasets on your computer?

Thank you in advance,

Jonas

On Mon, Jul 19, 2021 at 3:57 PM janet Chang @.***> wrote:

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1]

"================================================================================="

[1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study:

Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk"

[1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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janet-Chang commented 2 years ago

Thank you very much, Jonas:

Yes, it worked with R 3.6. Thanks for all your help.

I will remind the professor to cite your page and/or paper as reference in his upcoming publication. Thanks again.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Wednesday, July 21, 2021 4:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I tried running the GWIZ code using R v 4.1.0 and also got an error (albeit a slightly different one). Try running the code using R v 3. I am not entirely sure why, but I believe GWIZ is only compatible with R v 3. It should be possible to download multiple versions of R on your machine and switch between them so that you do not lose all of the packages you already have installed under your R v 4.

Let me know if that fixes anything!

All best,

Jonas

On Tue, Jul 20, 2021 at 11:59 AM janet Chang @.***> wrote:

Thanks a lot, Jonas:

I got all this from a professor, he is using your code on his population project, I am supporting his research at the computing center. Originally, he tried to run on his PC, and got the similar error. For convenience, I moved everything to the HPC cluster.

I used conda to install R version 4.1.0, pull the code from your github page directly on the cluster. The Data folder looked like this:

(Renv4II) @. Data]$ ls Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv (Renv4II) @. Data]$

If I open the file, they look like as attached on the cluster, typical csv file. I am also attaching those two csv files downloaded from the cluster.

I tried to change them into tab delimited file, didn't work. I also checked the other functions briefly, it is logistics regression, which shall accept non-numerical values. But the error message was complaining about linear regression lm.fit ?

Thanks again for all your help.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Tuesday, July 20, 2021 1:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Could you send me the csv data files you are working with? (i.e. Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv and Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv)

I just freshly pulled the code from github and was able to run it on my computer, so my first guess is that maybe something messed up the datasets on your computer?

Thank you in advance,

Jonas

On Mon, Jul 19, 2021 at 3:57 PM janet Chang @.***> wrote:

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1]

"================================================================================="

[1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study:

Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk"

[1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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jonaspatronjp commented 2 years ago

Perfect! Glad I could help. I will update the documentation when I get a chance to avoid others running into this problem as well.

Take care,

Jonas

On Wed, Jul 21, 2021 at 2:32 PM janet Chang @.***> wrote:

Thank you very much, Jonas:

Yes, it worked with R 3.6. Thanks for all your help.

I will remind the professor to cite your page and/or paper as reference in his upcoming publication. Thanks again.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Wednesday, July 21, 2021 4:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I tried running the GWIZ code using R v 4.1.0 and also got an error (albeit a slightly different one). Try running the code using R v 3. I am not entirely sure why, but I believe GWIZ is only compatible with R v 3. It should be possible to download multiple versions of R on your machine and switch between them so that you do not lose all of the packages you already have installed under your R v 4.

Let me know if that fixes anything!

All best,

Jonas

On Tue, Jul 20, 2021 at 11:59 AM janet Chang @.***> wrote:

Thanks a lot, Jonas:

I got all this from a professor, he is using your code on his population project, I am supporting his research at the computing center. Originally, he tried to run on his PC, and got the similar error. For convenience, I moved everything to the HPC cluster.

I used conda to install R version 4.1.0, pull the code from your github page directly on the cluster. The Data folder looked like this:

(Renv4II) @. Data]$ ls Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv (Renv4II) @. Data]$

If I open the file, they look like as attached on the cluster, typical csv file. I am also attaching those two csv files downloaded from the cluster.

I tried to change them into tab delimited file, didn't work. I also checked the other functions briefly, it is logistics regression, which shall accept non-numerical values. But the error message was complaining about linear regression lm.fit ?

Thanks again for all your help.

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Tuesday, July 20, 2021 1:07 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Could you send me the csv data files you are working with? (i.e. Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv and Combined analysis of 19 common validated type 2 diabetes susceptibility gene variants shows moderate discriminative value and no evidence.csv)

I just freshly pulled the code from github and was able to run it on my computer, so my first guess is that maybe something messed up the datasets on your computer?

Thank you in advance,

Jonas

On Mon, Jul 19, 2021 at 3:57 PM janet Chang @.***> wrote:

Thank you very much!

I really appreciate that!

Best regards

Janet

Janet Chang, PhD

Senior Scientist Office of Advanced Research Computing

Rutgers University

185 South Orange Ave. MSB C-630 Newark, NJ 07101 Tel. 973.972.1004

From: jonaspatronjp @.> Sent: Monday, July 19, 2021 5:55 PM To: jonaspatronjp/GWIZ-Rscript @.> Cc: janet Chang @.>; Author @.> Subject: Re: [jonaspatronjp/GWIZ-Rscript] linear regression / logistic regression? (#1)

Hi Janet,

I'm just writing to let you know that I have received your message and will try to figure out what is causing the error as soon as I get a chance!

All best,

Jonas

On Mon, Jul 19, 2021, 3:37 PM janet Chang, @.***> wrote:

When I run the GWAS_call_batch.R, using your example datasets in the Data folder, I got the following error:

"Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>"

Your help will be greatly appreciated. Thanks

Sincerely

Janet

PS. the following is the output

for (j in 1:length(files)){

source("./modeling/GWAS_functions.0,1,2genotype (attempt 4).R") genereteBatch(folderPath, folderOut, files[[j]]) studies <- dir(paste(filename, "/out", sep=""))

only csv files

studies <- studies[grep(".csv", studies)] source("./modeling/_modelingFunctions_lda.R") batchAnalysis(paste(filename, "/out", sep=""), resultsfilename, studies[[j]], verbose = FALSE, outerFolds = 3L, outerRep = 2L)#, classifier = "classif.logreg") studyname = substring(files[[j]], 1, 13) aucout[j,] <- c(studyname, aucanalysis) colnames(aucout) <- c("Study", "Simulated AUC")

} Resampling 1 studies: [1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" [1]

"================================================================================="

[1] "Assessing the Combined Impact of 18 Common Genetic Variants of Modest Effect Sizes on Type 2 Diabetes Risk.csv" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1559

$Hn [1] 3637

$Ds [1] 1701

$Dn [1] 2917

$hatOR [1] 1.360395

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1871

$Hn [1] 3325

$Ds [1] 1907

$Dn [1] 2711

$hatOR [1] 1.250084

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4417

$Hn [1] 779

$Ds [1] 4031

$Dn [1] 587

$hatOR [1] 1.211113

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4521

$Hn [1] 675

$Ds [1] 4111

$Dn [1] 507

$hatOR [1] 1.210623

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 572

$Hn [1] 4624

$Ds [1] 576

$Dn [1] 4042

$hatOR [1] 1.151988

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3066

$Hn [1] 2130

$Ds [1] 2860

$Dn [1] 1758

$hatOR [1] 1.130198

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1715

$Hn [1] 3481

$Ds [1] 1643

$Dn [1] 2975

$hatOR [1] 1.120961

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2131

$Hn [1] 3065

$Ds [1] 2012

$Dn [1] 2606

$hatOR [1] 1.110454

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1767

$Hn [1] 3429

$Ds [1] 1681

$Dn [1] 2937

$hatOR [1] 1.110695

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3638

$Hn [1] 1558

$Ds [1] 3324

$Dn [1] 1294

$hatOR [1] 1.100098

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1507

$Hn [1] 3689

$Ds [1] 1423

$Dn [1] 3195

$hatOR [1] 1.090258

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1040

$Hn [1] 4156

$Ds [1] 997

$Dn [1] 3621

$hatOR [1] 1.100294

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3118

$Hn [1] 2078

$Ds [1] 2846

$Dn [1] 1772

$hatOR [1] 1.070386

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 1923

$Hn [1] 3273

$Ds [1] 1783

$Dn [1] 2835

$hatOR [1] 1.070447

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4001

$Hn [1] 1195

$Ds [1] 3596

$Dn [1] 1022

$hatOR [1] 1.050916

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 3222

$Hn [1] 1974

$Ds [1] 2886

$Dn [1] 1732

$hatOR [1] 1.020869

$model [1] "recessive"

[1] "recessive model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 4729

$Hn [1] 467

$Ds [1] 4218

$Dn [1] 400

$hatOR [1] 1.041344

$model [1] "dominant"

[1] "dominant model" phenotype dataset accession control_size case_size risk_allele_freq OR 1 n/a n/a rs7903146 2598 2309 0.30 1.36 2 n/a n/a rs5219 2598 2309 0.36 1.25 3 n/a n/a rs10811661 2598 2309 0.85 1.21 4 n/a n/a rs1801282 2598 2309 0.87 1.21 5 n/a n/a rs2641348* 2598 2309 0.11 1.15 6 n/a n/a rs564398 2598 2309 0.59 1.13 7 n/a n/a rs4402960 2598 2309 0.33 1.12 8 n/a n/a rs8050136 2598 2309 0.41 1.11 9 n/a n/a rs10946398 2598 2309 0.34 1.11 10 n/a n/a rs13266634 2598 2309 0.70 1.10 11 n/a n/a rs7961581 2598 2309 0.29 1.09 12 n/a n/a rs12779790 2598 2309 0.20 1.10 13 n/a n/a rs10010131 2598 2309 0.60 1.07 14 n/a n/a rs757210 2598 2309 0.37 1.07 15 n/a n/a rs4607103 2598 2309 0.77 1.05 16 n/a n/a rs1111875 2598 2309 0.62 1.02 17 n/a n/a rs7578597 2598 2309 0.91 1.04 18 n/a n/a rs864745 2598 2309 0.50 1.00 model 1 dominant 2 recessive 3 dominant 4 recessive 5 dominant 6 recessive 7 dominant 8 recessive 9 dominant 10 recessive 11 dominant 12 recessive 13 dominant 14 recessive 15 dominant 16 recessive 17 dominant 18 recessive $Hs [1] 2598

$Hn [1] 2598

$Ds [1] 2309

$Dn [1] 2309

$hatOR [1] 1

$model [1] "recessive"

[1] "recessive model" [1] "done!!! :)" [1] "-------------------------------------------------------------------" [1] "Analizing study:

Assessing_the_Combined_Impact_of_18_Common_Genetic_Variants_of_Modest_Effect_Sizes_on_Type_2_Diabetes_Risk"

[1] "-------------------------------------------------------------------" Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y' In storage.mode(v) <- "double" : NAs introduced by coercion>

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