Question

GWAStools error when performing regression analysis

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Entering edit mode

thye • 0

@thye-19883

Last seen 5.2 years ago

Hello ,

I successfully imported PLINK binary files with the SNPRelate snpgdsBED2GDS function for analysis with GWAStools package. Unfortunately, when I try to perform an association analysis with the assocRegression module of the GWAStools I get the following error:

> fam.fn <-  "extdata/zztest.fam"
> bim.fn <-  "extdata/zztest.bim"
> bed.fn <-  "extdata/zztest.bed"
> gdsfile <- "snps4.gds"
> snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, gdsfile, family=TRUE, cvt.chr="int", verbose=TRUE)
> gds <- GdsGenotypeReader(gdsfile, YchromCode=24L, XYchromCode=25L)
>assoc = assocRegression(gds, outcome="status", model.type="logistic", snpStart=1, snpEnd=50)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘hasSex’ for signature ‘"GdsGenotypeReader"

Any help is appreciated.

With kind regards,

Thorsten

GWAStools association GdsGenotypeReader hasSex • 563 views

ADD COMMENT • link updated 5.2 years ago by Martin Morgan 25k • written 5.2 years ago by thye • 0

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Entering edit mode

Finally found the solution. Had to add sex and phenotype data from the PLINK FAM-file to the gds genotype file in an extra step.

FAM<-read.table(file="extdata/zztest.fam", header=FALSE)

names(FAM)=c("FAMID", "ID", "FA","MO","SEX","STATUS")

mydat <- data.frame(scanID = FAM$ID, famID=FAM$FAMID,SEX=FAM$SEX, STATUS = FAM$STATUS)

scanAnnotT=ScanAnnotationDataFrame(mydat)

scanAnnot <- ScanAnnotationDataFrame(mydat)

genoDATA <- GenotypeData(gds, scanAnnot = scanAnnotT)

assoc = assocRegression(genoDATA, outcome="STATUS", model.type="logistic", snpStart=1, snpEnd=50)

ADD REPLY • link 5.2 years ago thye • 0