.gds format for SAIGEgds
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Entering edit mode
16 months ago
abyousaf • 0

Hello everyone,

I am trying to use SAIGEgds. I originally had chromosome-separated VCF files that I combined into .gds format using SNPRelate's snpgdsVCF2GDS and successfully generated a .gds file.

I then tried inputting it into SAIGEgds as such:

genofile <- snpgdsOpen("C:\\Users\\John\\Desktop\\QC_VCF.gds")

glmm <- seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, genofile, trait.type="binary")

but got the following error:

"Error in seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, genofile, trait.type = "binary", : is.character(gdsfile) | inherits(gdsfile, "SeqVarGDSClass") is not TRUE"

Did I use the wrong R package to make the .gds file? Should I instead have used SeqArray's seqVCF2GDS

SAIGE .gds • 385 views
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