weizhouUMICH SAIGE issues

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0

187 stars 71 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Step 1 with sparse GRM gets stuck on "use sparse kinship to fit the model"

#447 alix-lacoste closed 1 month ago
1
Pre-computed group files for UKB WES

#446 aanighoro opened 3 months ago
0
The appropriate sample size for continuous and binary traits analysis in SAIGE-GENE+

#445 jxcao98 opened 6 months ago
0
Error running Step 1 on UKBB dataset.

#444 nanjalaruth opened 7 months ago
0
Chromosome coding UKBB

#443 nandobonf opened 7 months ago
0
R CMD INSTALL SAIGE

#442 yang285 opened 7 months ago
0
Error in mainRegionInCPP

#441 willow9505 opened 8 months ago
0
Trying to get LOCO=True to work

#440 Ankeet3 opened 9 months ago
0
Step1, sorting of sample ids

#439 Ankeet3 opened 9 months ago
0
createSparseGRM script (step0) doesn’t work

#438 omrak opened 10 months ago
0
How do you create the SparseSigmafile?

#437 Ruedog opened 10 months ago
0
Should this SAIGE be closed since you have a new SAIGE page?

#436 StripelessWatermelon opened 11 months ago
0
possible issue with categorical variables used as covariates?

#435 brettva opened 11 months ago
0
createSparseGRM error

#434 BIjoy92 opened 11 months ago
0
samples in geno file do not have phenotypes

#433 nm15336 closed 11 months ago
0
Can dominant model be used in single variant test?

#432 koko-mo-127 opened 1 year ago
0
Can't install

#431 Welz2 opened 1 year ago
0
Error at step2 on chrX

#430 eightYao2 opened 1 year ago
0
Error in getopt(spec = spec, opt = args) : long flag "bedFile" is invalid

#429 jingydz opened 1 year ago
4
SAIGE-GENE+ install

#428 jingydz closed 1 year ago
3
Error creating sparseGRM using 200k WES

#427 ajlee21 opened 1 year ago
0
floating point exception raised during step2 SPAtests

#426 mstapylton opened 1 year ago
0
Using SAIGE on correlated phenotypic data

#425 AudeIkuzwe04 opened 1 year ago
0
Why are some parameters invalid when fitting the step1 model of set-based test?

#424 xuqian-007 closed 1 year ago
0
Empty Step 1 SAIGE files

#423 AudeIkuzwe04 opened 1 year ago
0
Error in if (pval != 0 && pval.noadj/pval > 10^3)

#422 ilovemr opened 1 year ago
1
heterogeneity of effect

#421 psychrb opened 1 year ago
0
Running SAIGE with small sample

#420 kbsssu opened 1 year ago
0
SAIGE install via Conda configuration failure (failed to build statgen/savvy)

#419 krishnaxamin opened 1 year ago
2
Error Message: Error in setSAIGEobjInCPP(t_XVX = obj.model$obj.noK$XVX, t_XXVX_inv = obj.model$obj.noK$XXVX_inv

#418 Jeffleecy opened 1 year ago
2
Interpreting the BETA output from SAIGE

#417 adanordeidet opened 1 year ago
0
Download failed with error 503 for: //github.com/statgen/savvy/archive/v2.1.0.tar.gz

#416 7JVST closed 1 year ago
0
Failure with r-saige package installation from Bioconda

#415 zcebeci opened 1 year ago
0
是否可以在windowns系统运行？

#414 sheshen22 opened 1 year ago
0
SAIGE error step2

#413 LMoolhuijsen opened 1 year ago
1
Download failed with error 404 for: //zlib.net/zlib-1.2.11.tar.gz

#412 psammarco closed 1 year ago
1
Error message: "ERROR! The first variance component parameter estimate is 0"

#411 dkimsjch opened 1 year ago
6
No markers found --SPAGMMATtest

#410 medinacarolina opened 1 year ago
0
p-values illogically small (10^-280) in conditional analysis

#409 mallorydownie opened 2 years ago
3
Missing --qCovarColList flag from step1_fitNULLGLMM.R wrapper script?

#408 samuelejones opened 2 years ago
2
SAIGE step2 sampleID error

#407 crystalorangeZR opened 2 years ago
0
permutation test to phewas analysis to decrease the burden of multiple testing correction

#406 Shicheng-Guo closed 2 years ago
1
Effect size

#405 mkierczak closed 2 years ago
1
segfaults on newer SAIGE in Docker. Older versions still work.

#404 pettyalex closed 2 years ago
1
problem/error with running conditional analysis

#403 ruthchia closed 2 years ago
2
Warning: no sample level data available

#402 michelemarongiu79 closed 2 years ago
1
Issues with --useSparseGRMtoFitNULL=TRUE

#401 eugenegardner closed 2 years ago
1
step2_SPAtests.R doesn't analyze SNPs that are expected to be analyzed

#400 gurinovich closed 2 years ago
2
including rare variants in GRM decrease statistical power to identify novel targets?

#399 Shicheng-Guo closed 2 years ago
1
numRandomMarkerforSparseKin and relatednessCutoff in GRM generation

#398 Shicheng-Guo closed 2 years ago
1