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privefl
/
bigsnpr
R package for the analysis of massive SNP arrays.
https://privefl.github.io/bigsnpr/
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LDPred2 halts when *snp_ldsc()* is called
#364
jspatane
closed
2 years ago
3
Seeking help for LDpred2 Implementation: resulting scores do not correlate with phenotype
#363
JiayiHelenZhou
closed
1 year ago
8
Help understanding the output of LDpred2
#362
kathrynfreeman
closed
2 years ago
4
Error in format_snp_id(snp_id) in snp_readBGEN and snp_readBGI
#361
JasperHof
closed
2 years ago
5
Genetic correlation using LDpred2 summary statistics
#360
alek0991
closed
2 years ago
7
Trouble getting the model performance in LDpred2
#359
Mahantesh-Biradar
closed
2 years ago
5
snp_asGeneticPos kept giving the same error message
#358
YunfengRuan
closed
2 years ago
23
Using snp_readBGEN on dnanexus RStudio server
#357
edobrijevic
closed
2 years ago
10
GWAS summary statistics from a mixed model
#356
alek0991
closed
2 years ago
1
remove duplicates leads to index larger than maximal 46367
#355
AlisaBIG
closed
2 years ago
8
reversed sign of Beta
#354
alek0991
closed
2 years ago
8
UKBB and hapmap3 variants
#353
alek0991
closed
2 years ago
4
Add cross-trait LDSC
#352
jean997
opened
2 years ago
9
Can we analyse PRS from LDpred2 and PRS from (stacked) clumping and thresholding together?
#351
jianvhuang
closed
2 years ago
2
Load SFBM (.sbk) correlation matrix from disk
#350
alek0991
closed
2 years ago
2
Quality control of summary statistics exclude (almost) all SNPs
#349
jianvhuang
closed
2 years ago
9
PRS coefficients
#348
Robbie-RL
closed
2 years ago
7
h2 calculated to be negative value
#347
AlisaBIG
closed
2 years ago
2
The estimated beta is all NA when using the function snp_ldpred2_grid()
#345
siawhui
closed
2 years ago
1
snp_cor() sometimes outputs values outside of [-1, 1]
#344
privefl
closed
1 year ago
0
Error using snp_fastImpute
#343
watplatt
closed
2 years ago
6
How to save a .bed,.bim.,.fam set from an .rdx like object?
#342
watplatt
closed
2 years ago
2
Questions about QC Process
#341
jfrank94
closed
2 years ago
5
Discovered outliers detected in different iterations of SVD
#340
fmadani
closed
2 years ago
1
mismatched allele1 compared to `.bed` file converted using plink2
#339
caimiao0714
closed
2 years ago
8
heritability in function snp_simuPheno()
#338
harryyiheyang
closed
2 years ago
5
BackingFile creation
#337
dzimmerman-amc
closed
2 years ago
3
Precision concerning bed_cprodVec
#336
JasmRicard
closed
2 years ago
2
Summary statistics comparison
#335
rameez500
closed
2 years ago
5
Add reproducibility to LDpred2
#334
privefl
closed
2 years ago
0
NA values in the resulting correlation matrix
#333
alejocrojo09
closed
2 years ago
5
Run snp_ldpred2_grid in a for loop trigger Warning: stack imbalance in 'for'
#332
xyang619
closed
2 years ago
9
A small number of matched variants causes small SNP heritability estimate
#331
singh-p
closed
2 years ago
4
adjusted beta for PRS model taking too long
#330
Charlkb
closed
2 years ago
2
Scale of beta in the source code of LDpred2.R is not the same as described in the original paper
#329
xyang619
closed
2 years ago
2
A minor modifications in naming data variables
#328
fmadani
closed
2 years ago
1
z-value used as z-score
#327
fmadani
closed
2 years ago
1
Power and accuracy of PRSs
#326
rameez500
closed
2 years ago
1
snp_modifyBuild gives truncated results
#325
yidingdd
closed
2 years ago
4
Issues with LDpred2 crashing when using a large number of SNPs
#324
lindseysinclair
closed
2 years ago
3
Settings of snp_ldsplit()
#323
LucieTroubat
closed
2 years ago
2
Genome Build test in bigsnpr
#322
fmadani
closed
2 years ago
1
Scales of polygenic risk score distributions
#321
johannfaouzi
closed
2 years ago
10
Extract betas from lassosum2
#320
Fnyasimi
closed
2 years ago
11
Feature request: modified matrix product operations
#319
garyzhubc
closed
2 years ago
1
Computing pred_auto with LD reference
#318
sandralapinska
closed
2 years ago
4
Is it possible to compute fuzzy relational product with this package?
#317
garyzhubc
closed
2 years ago
4
Clumping with LD matrix directly
#316
jordanero
closed
2 years ago
4
Trouble with obj.bed formatting
#315
AlePilHen
closed
2 years ago
2
Error: 'infos.pos' is not sorted.
#314
forevertl
closed
2 years ago
3
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