Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed

[gpsccs]

Describe the bug when I try to use the function of readStandardGenotypes(), it occour this error, I wonder what the problem is?

To Reproduce

genotypes <- readStandardGenotypes(N=1000, filename = genotypefile,format="plink", verbose=TRUE,sampleID = "SN") Error in .rowNamesDF<-(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value when setting 'row.names': ‘.’

Looking forward to your answers

[HannahVMeyer]

Please provide your sessionInfo(). What is the genotype file you are trying to read?

[gpsccs]

Please provide your sessionInfo(). What is the genotype file you are trying to read?

sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

attached base packages: [1] stats graphics grDevices utils datasets methods
[7] base

other attached packages: [1] PhenotypeSimulator_0.3.3 sim1000G_1.40
[3] readr_1.3.1 stringr_1.4.0
[5] hapsim_0.31 caret_6.0-84
[7] ggplot2_3.2.1 G2P_1.1.0
[9] ROCR_1.0-7 gplots_3.0.1.1
[11] hglm_2.2-1 hglm.data_1.0-1
[13] sp_1.3-1 impute_1.60.0
[15] sommer_4.0.8 crayon_1.3.4
[17] lattice_0.20-38 MASS_7.3-51.4
[19] brnn_0.7 Formula_1.2-3
[21] pls_2.7-2 snowfall_1.84-6.1
[23] snow_0.4-3 rrBLUP_4.6
[25] randomForest_4.6-14 spls_2.2-3
[27] glmnet_2.0-18 foreach_1.4.7
[29] Matrix_1.2-17 e1071_1.7-2
[31] pROC_1.15.3 PRROC_1.3.1
[33] BGLR_1.0.8 data.table_1.12.6

loaded via a namespace (and not attached): [1] nlme_3.1-139 bitops_1.0-6 lubridate_1.7.4
[4] tools_3.6.0 backports_1.1.5 R6_2.4.0
[7] rpart_4.1-15 KernSmooth_2.23-15 lazyeval_0.2.2
[10] BiocGenerics_0.32.0 colorspace_1.4-1 nnet_7.3-12
[13] withr_2.1.2 tidyselect_0.2.5 compiler_3.6.0
[16] caTools_1.17.1.2 scales_1.0.0 R.utils_2.9.0
[19] pkgconfig_2.0.3 rlang_0.4.1 rstudioapi_0.10
[22] generics_0.0.2 zoo_1.8-6 gtools_3.8.1
[25] dplyr_0.8.3 ModelMetrics_1.2.2 R.oo_1.23.0
[28] magrittr_1.5 Rcpp_1.0.2 munsell_0.5.0
[31] R.methodsS3_1.7.1 stringi_1.4.3 yaml_2.2.0
[34] zlibbioc_1.32.0 plyr_1.8.4 recipes_0.1.7
[37] grid_3.6.0 parallel_3.6.0 gdata_2.18.0
[40] snpStats_1.36.0 cowplot_1.0.0 splines_3.6.0
[43] hms_0.5.2 zeallot_0.1.0 pillar_1.4.2
[46] optparse_1.6.4 reshape2_1.4.3 codetools_0.2-16
[49] stats4_3.6.0 glue_1.3.1 vctrs_0.2.0
[52] getopt_1.20.3 gtable_0.3.0 purrr_0.3.3
[55] AlphaSimR_0.11.0 assertthat_0.2.1 gower_0.2.1
[58] prodlim_2019.10.13 class_7.3-15 survival_2.44-1.1
[61] timeDate_3043.102 truncnorm_1.0-8 tibble_2.1.3
[64] iterators_1.0.12 lava_1.6.6 ipred_0.9-9

I was trying to read a .bed file as the genotype files and it was just converted from VCF by plink, the format of the file should be right I think

[HannahVMeyer]

can you run:

genotypes <- snpStats::read.plink(bed = genotypefile)
length(genotypes$fam$member)
length(unique(genotypes$fam$member))
length(genotypes$map$snp.name)
length(unique(genotypes$map$snp.name))

[gpsccs]

Nope. the same error occoured. Error in.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique value when setting 'row.names': ‘.’

length(genotypes$fam$member) [1] 0 length(unique(genotypes$fam$member)) [1] 0 length(genotypes$map$snp.name) [1] 0 length(unique(genotypes$map$snp.name)) [1] 0`

[gpsccs]

Or may I send the .bed .bim and .fam file to you?

[HannahVMeyer]

Ok, so the problem is not within a function of PhenotypeSimulator, but rather occurs in the snpStats::read.plink function. I am suspecting the problem lies in your .fam and .bim file that might not have been created properly in the conversion process? What do your sample and SNP ids look like?

[HannahVMeyer]

Or may I send the .bed .bim and .fam file to you?

Yes, feel free to send

[gpsccs]

Well, I think I know what the problem is. When I use plink to convert .vcf to .bed, there are some details lost. the bim file are just like: 1 . 0 652 A G I turn to vcftools for help and the function can run properly. which bim file like: 1 chr1:652 0 652 A G

However, another error occurred. `

genotypes <- readStandardGenotypes(N=300, filename = genotypefile,format="plink", verbose=TRUE,sampleID = "SN") genotypes_sd <- standardiseGenotypes(genotypes$genotypes) Error in FUN(X[[i]], ...) : SNP vector contains alleles not encoded as 0, 1 or 2 ` Did I miss something?

[HannahVMeyer]

Do you have missing values in your genotypes? Can you run

unique(as.vector(genotypes$genotypes))

[gpsccs]

Do you have missing values in your genotypes? Can you run

unique(as.vector(genotypes$genotypes))

Yes, the output are as follow. what should I do?

unique(as.vector(genotypes$genotypes)) [1] 0 2 1 NA

[HannahVMeyer]

gamason pointed to a similar issue last month: https://github.com/HannahVMeyer/PhenotypeSimulator/issues/17#issuecomment-537724570

I would follow the advise I gave there, install the development version of the PhenotypeSimulator and use impute=TRUE in standardiseGenotypes, to impute the missing genotypes. Alternatively, you can remove all SNPs with missing genotypes or use another imputation method of your choice prior to using PhenotypeSimulator. As I outlined here: https://github.com/HannahVMeyer/PhenotypeSimulator/issues/17#issuecomment-537724570 I believe imputation of missing values will be most useful though.

[gpsccs]

Thank you very much for your kind reply. I will try it later. Hope a good day for you.

[HannahVMeyer]

Happy to help, let me know if this solved your problem

[HannahVMeyer]

Closing this now, feel free to re-open if issue persists.