privefl bigsnpr issues - Githubissues

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

https://privefl.github.io/bigsnpr/

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issues

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How to code genotypes 0.01, 0.2, etc (NB these are not dosages but something else) as missing?

#505 RPorneso closed 1 week ago
3
Is it possible to call `big_univLogReg` on simulated data?

#504 garyzhubc opened 2 weeks ago
1
bed_projectPCA pre processing

#503 RoniHaas closed 4 days ago
4
*_autoSVD now work without call to library()

#502 dramanica closed 1 month ago
0
`snp_autoSVD()` only works after a `library("bigsnpr")` call

#501 dramanica closed 1 month ago
4
Error in makePSOCKcluster when calling snp_ldpred2_auto

#500 shachideshpande closed 1 month ago
2
scale of MCMC sampling of beta

#499 yidingdd opened 1 month ago
3
Should error when using a correlation matrix with NA / NaNs values

#498 privefl opened 1 month ago
0
Predicting phenotype after running LDpred2

#497 shachideshpande closed 1 month ago
18
Error in step #3 of projecting PC scores on new data

#496 ozandikilitas opened 2 months ago
15
LDpred2: running auto model gives NAs for all beta_est

#495 SaraBecelaere closed 2 months ago
18
Handle insertions/deletions coded as I/D in snp_match()

#494 privefl opened 2 months ago
2
Would it be possible to release 1.12.6?

#493 stefcardinale opened 2 months ago
1
[snp_modifyBuild] add [local.chain]

#492 Hugolyu closed 2 months ago
3
Getting this error while trying to convert from hg19 to hg38

#491 znayema closed 2 months ago
8
Hint for creating proper bed file from ped for polygenic risc score

#490 nalalenny closed 2 months ago
7
No $fam created with snp_readBGEN(). How to map genotype back to individuals?

#489 el-rs closed 2 months ago
5
Error when mapping file: Invalid argument.

#488 privefl closed 3 months ago
5
Script example-with-provided-LD.R does not work

#487 alhannae closed 3 months ago
2
Error when running example-with-provided-LD.R

#486 alhannae closed 3 months ago
6
Imputation for haploid organisms

#485 adomron24 opened 3 months ago
2
Question about LDpred2 on PRS

#484 wendy-xiaozong closed 3 months ago
2
Is it possible to plot p-values with multiple corrections?

#483 garyzhubc closed 4 months ago
3
correlation matrix

#482 alhannae closed 3 months ago
6
How to get the avaliable snp list with corrected beta used in LDpred2-auto module

#481 koujiaodahan opened 4 months ago
2
Error: 'chi2' should have only positive values. in snp_ldsc()

#480 koujiaodahan closed 4 months ago
5
Loading Chromosome X data (nonPAR) using bigsnpr

#479 JasperHof closed 3 months ago
12
Got only NA in calculating PRS

#478 KirakiraZLY closed 2 months ago
10
Problem with snp_match()

#477 girarn closed 4 months ago
2
Why do I get zero p-values?

#476 garyzhubc closed 4 months ago
7
Error in xtfrm.data.frame(x) : cannot xtfrm data frames

#475 garyzhubc closed 4 months ago
1
Running LDpred2 without internet server access

#474 uki-uiu closed 1 month ago
8
LDpred2-auto for EWAS

#473 KristofferSandas opened 5 months ago
31
LD calculation: NA or NAN values in the resulting correlation matrix

#472 JNajar closed 5 months ago
17
standalone LDpred2 command line script

#471 espenhgn closed 5 months ago
4
See if could make snp_colstats() faster

#470 privefl opened 6 months ago
0
Clumping option

#469 msong97 closed 6 months ago
4
comparison of PCA from bigsnpr and PLINK

#468 ndimou closed 7 months ago
8
Error in { : task 1 failed - "Incorrect number of arguments (17), expecting 16 for '_bigsnpr_ldpred2_gibbs_auto'"

#467 jfertaj closed 2 months ago
2
Is it the correct way to annotate Manhattan plot with significance level?

#466 garyzhubc closed 7 months ago
3
Related sample

#465 JuanJoMV closed 7 months ago
2
Error in snp_ldsc

#464 KK520520 closed 7 months ago
5
Error: Tested 13641 < 13641. Subscript out of bounds.

#463 DUAN-GAO closed 2 months ago
5
EUR reference panel for GRChr38 to run LDpred2

#462 habraham17 closed 2 months ago
2
negative heritablity result

#461 DUAN-GAO closed 7 months ago
3
Using bigsnpr C++ headers in my package

#460 kristjanmoore opened 8 months ago
5
Getting started (FBM)

#459 DobraVila closed 4 months ago
1
Is it possible to do snp_manhattan with position on the x-axis instead of chromosome?

#458 garyzhubc closed 4 months ago
1
PCA calculation: outlier removal

#457 aepacker closed 4 months ago
1
LD score regression, variable number of ld_size

#456 HerefordGuy closed 2 months ago
8