privefl bigsnpr issues - Githubissues

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

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

196 stars 44 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Ancestry estimator applied to UKB using PCs calculated

#523 gtdoctor opened 4 days ago
1
Use the genotype matrix for another library

#522 garyzhubc opened 6 days ago
4
(fast) matrix operations on bigsnp_obj genotype matrix

#521 garyzhubc closed 6 days ago
1
Outlier detection scaling by eigenvalue/ S vector ; scales PCA scores

#520 gtdoctor closed 1 week ago
2
Data file format

#519 vdvornyk1 opened 4 weeks ago
3
LD Metrics Using 1000 Genomes and Beta Values Returning NA

#518 Taewoong-Ha opened 1 month ago
4
Different PGS for the same person

#517 trinetn closed 1 month ago
4
I keep getting PGSs equal 0

#516 trinetn closed 1 month ago
12
Some failures in tests [ FAIL 13 | WARN 0 | SKIP 1 | PASS 174 ]

#515 barracuda156 opened 2 months ago
5
How to get sample ids out of a bigsnpr object?

#514 garyzhubc opened 3 months ago
1
Issue with the loop in the code

#513 khujithrajueni opened 3 months ago
3
'chi2' and 'ld_score' should have the same length

#512 koujiaodahan closed 3 months ago
3
How to deal "missing value error" on imputed genotypes data

#511 panqinglzmc opened 3 months ago
7
snp_match removed ambiguous SNPs

#510 koujiaodahan closed 3 months ago
4
About the INFO value in Quality Control of GWAS summary statistics

#509 koujiaodahan opened 4 months ago
2
Invalid pointer with `snp_ldsplit`

#508 biona001 closed 4 months ago
5
AUC error

#507 alambard closed 4 months ago
18
how to handle ldsc with negative h2 value?

#506 SangGold opened 4 months ago
2
How to code genotypes 0.01, 0.2, etc (NB these are not dosages but something else) as missing?

#505 RPorneso closed 5 months ago
3
Is it possible to call `big_univLogReg` on simulated data?

#504 garyzhubc closed 3 months ago
1
bed_projectPCA pre processing

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

#502 dramanica closed 5 months ago
0
`snp_autoSVD()` only works after a `library("bigsnpr")` call

#501 dramanica closed 5 months ago
4
Error in makePSOCKcluster when calling snp_ldpred2_auto

#500 shachideshpande closed 6 months ago
2
scale of MCMC sampling of beta

#499 yidingdd closed 3 months ago
3
Should error when using a correlation matrix with NA / NaNs values

#498 privefl opened 6 months ago
0
Predicting phenotype after running LDpred2

#497 shachideshpande closed 6 months ago
18
Error in step #3 of projecting PC scores on new data

#496 ozandikilitas opened 6 months ago
16
LDpred2: running auto model gives NAs for all beta_est

#495 SaraBecelaere closed 7 months ago
18
Handle insertions/deletions coded as I/D in snp_match()

#494 privefl opened 7 months ago
2
Would it be possible to release 1.12.6?

#493 stefcardinale opened 7 months ago
1
[snp_modifyBuild] add [local.chain]

#492 Hugolyu closed 7 months ago
3
Getting this error while trying to convert from hg19 to hg38

#491 znayema closed 7 months ago
8
Hint for creating proper bed file from ped for polygenic risc score

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

#489 el-rs closed 7 months ago
5
Error when mapping file: Invalid argument.

#488 privefl closed 8 months ago
5
Script example-with-provided-LD.R does not work

#487 alhannae closed 8 months ago
2
Error when running example-with-provided-LD.R

#486 alhannae closed 8 months ago
6
Imputation for haploid organisms

#485 adomron24 opened 8 months ago
2
Question about LDpred2 on PRS

#484 jueqiw closed 8 months ago
2
Is it possible to plot p-values with multiple corrections?

#483 garyzhubc closed 8 months ago
3
correlation matrix

#482 alhannae closed 8 months ago
6
How to get the avaliable snp list with corrected beta used in LDpred2-auto module

#481 koujiaodahan opened 9 months ago
2
Error: 'chi2' should have only positive values. in snp_ldsc()

#480 koujiaodahan closed 9 months ago
5
Loading Chromosome X data (nonPAR) using bigsnpr

#479 JasperHof closed 8 months ago
12
Got only NA in calculating PRS

#478 KirakiraZLY closed 7 months ago
10
Problem with snp_match()

#477 girarn closed 9 months ago
2
Why do I get zero p-values?

#476 garyzhubc closed 9 months ago
7
Error in xtfrm.data.frame(x) : cannot xtfrm data frames

#475 garyzhubc closed 9 months ago
1
Running LDpred2 without internet server access

#474 uki-uiu closed 6 months ago
8