Question: Trouble reading plink (.raw) file into R (adegent)
gravatar for sryan6
4.5 years ago by
United States
sryan60 wrote:

I have converted a vcf file to the plink format

plink --file Variants --allow-no-sex
plink --file Variants --recodeA --out VariantsA --allow-no-sex
plink --file Variants --recode12 --out Variants12 --allow-no-sex


and tried to read these files into R using: <- read.PLINK(file="VariantsA.raw", parallel=FALSE)


but get the following error

Error in checkAtAssignment("SNPbin", "ploidy", "numeric") : 
  assignment of an object of class “numeric” is not valid for @‘ploidy’ in an object of class “SNPbin”; is(value, "integer") is not TRUE


Any help on what might be causing this would be much appreciated. I have looked through the vcf, ped, and raw file but can't seem to find anything wrong


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