Hi all,

I am trying to use the SKAT package in R for rare variant analysis. I am getting this error using this function to generate the SSD: Error in if (SetID1 != SetID2) { : missing value where TRUE/FALSE needed.

Here is the code:

>Generate_SSD_SetID(File.Bed, File.Bim, File.Fam, File.SetID, File.SSD, File.Info, Is.FlipGenotype=TRUE)
Check duplicated SNPs in each SNP set
Error in if (SetID1 != SetID2) { : missing value where TRUE/FALSE needed

I removed all duplicates and NAs from my setID file before using this function. Any help would be much appreciated.