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privefl
/
bigsnpr
R package for the analysis of massive SNP arrays.
https://privefl.github.io/bigsnpr/
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LD score regression, variable number of ld_size
#456
HerefordGuy
closed
2 months ago
8
Error in if (cost > max_cost) return(NULL)
#455
AlisaBIG
closed
8 months ago
6
snp_subset does not work when $fam is not there
#454
privefl
closed
8 months ago
1
`Error in `db_query_fields.DBIConnection()`: ! Can't query fields.`
#453
garyzhubc
closed
2 months ago
13
Is there a way to access LD structure via bigsnpr?
#452
garyzhubc
closed
8 months ago
5
Inference with LDpred2-auto
#451
beradan
closed
9 months ago
4
Duplicate rsids
#450
garyzhubc
closed
8 months ago
6
Error running snp_readBGEN/BGI: "Wrong format of some variants"
#449
JasperHof
closed
9 months ago
6
Error in running snp_readBed
#448
Rui127
closed
8 months ago
3
Can I use the external hg38 genetic_map file directly instead of using snp_asGeneticPos for interpolation?
#447
zbjbiubiubiu
closed
8 months ago
5
`Integer overflow` warning in `snp_cor` function
#446
filosi
closed
9 months ago
7
LDpred2: error in rowMeans on supercomputer cluster but not in R studio
#445
SaraBecelaere
closed
8 months ago
3
"NA or NaN values in the resulting correlation matrix."
#443
JNajar
closed
8 months ago
8
NA when running snp_ldpred2_grid
#440
kkleinoros
closed
8 months ago
3
LDpred2 PRS for one outcome?
#441
JNajar
closed
10 months ago
3
Memory size issues in snp_cor()
#439
kkleinoros
closed
10 months ago
10
Where to get SNP IDs corresponding to LDpred2 effect sizes?
#438
isobel16
closed
10 months ago
6
NAs with LDpred2 using UKBB and Finngen sumstats
#437
Herest
closed
10 months ago
6
Clumping without genotype data ?
#436
eliorzou
closed
11 months ago
5
Number of SNPs and their wights used for final PRS calculation
#435
Mahantesh-Biradar
closed
1 year ago
2
Integer overflow warning in snp_cor()
#434
fmorgante
closed
12 months ago
18
MCMCchain not converging
#433
xuxwen
closed
10 months ago
7
LDpred2 issue: All NAs in the final PRS file
#432
ShoaibBME
closed
10 months ago
5
Error in (function (cl, name, valueClass) : assignment of an object of class “NULL” is not valid for @‘i’ in an object of class “dsCMatrix”; is(value, "integer") is not TRUE
#431
Mahantesh-Biradar
closed
1 year ago
18
`ncores` option is ignored in `snp_fastImpute`
#430
domiden
closed
10 months ago
9
Heritability
#429
JuanJoMV
closed
1 year ago
4
Re-use .sbk file
#428
fmorgante
closed
1 year ago
6
NA in LDSC
#427
SoleilChenxu
closed
10 months ago
4
Is it possible to look at the sample ids from bigsnp_obj?
#426
garyzhubc
closed
1 year ago
2
LDSC heritability
#425
lingjoyo
closed
1 year ago
4
error from : corr$add_columns(corr0, nrow(corr))
#424
SoleilChenxu
closed
1 year ago
6
LDpred2, snp_ldpred2_auto outputs NAs
#423
lingjoyo
closed
1 year ago
3
No such file: tmp-data/chr2.OMNI.interpolated_genetic_map.gz
#422
Deleetdk
closed
1 year ago
2
Inflated Q-Q
#421
boseb
closed
1 year ago
2
Unusually High h2est Values: Exceeding 1 and Reaching up to 2 or 3
#420
PEWilliamZhou
opened
1 year ago
27
Simulating multiple genetically correlated phenotypes
#419
fmorgante
opened
1 year ago
7
OpenMP flag is not passed
#418
barracuda156
closed
1 year ago
1
Possible to apply bigsnpr outlier detection functions to PCA produced by a different program?
#417
TeresaPegan
closed
1 year ago
2
Error in rowMeans(sapply(multi_auto[keep], function(auto) auto$beta_est)) : 'x' must be an array of at least two dimensions
#416
xuxwen
closed
1 year ago
20
Slow running
#415
szhang1112
closed
1 year ago
19
Error in if (max(abs(pred - pred0)) < 1e-06) break
#414
Mahantesh-Biradar
closed
1 year ago
7
List of used SNPs
#444
AbrahamVanDeWalle
closed
10 months ago
1
Running LDpred2 auto with reference sample
#413
lm380-r
closed
1 year ago
4
Delete backing files and folders?
#412
TongYu37
closed
1 year ago
2
LD reference for HapMap3+ variants
#411
johannfaouzi
closed
1 year ago
2
Suggested model with no individual-level training data
#410
Fiwx
closed
1 year ago
3
indexing beta_auto in per chromosome computation
#409
TC-gu
closed
1 year ago
7
Error in { : task 1 failed - "L-BFGS-B needs finite values of 'fn'"
#408
Mahantesh-Biradar
closed
1 year ago
14
Using own correlation matrix of LD values.
#407
boseb
closed
1 year ago
2
LDPred2 with custom reference panel
#406
sourena-s
closed
1 year ago
21
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