Go to page http://zzz.bwh.harvard.edu/plink/profile.shtml and follow the help to generate a basic allele score using your independently associated SNPs. Use R to make the myprofile.rawfile required.
I am unable to generate .raw file which will contain allele score I have tried this script: results_2049669_adjusted <- read.table("results_2049669.assoc.linear.adjusted", header=T) #display first 15 SNPs results_2049669_adjusted [1:15,] system("plink_mac/plink --bfile BB5707 --clump results_2049669.assoc.linear --clump-p1 5e-08 --clump-p2 0.05 --clump-r2 0.1 --clump-kb 250 --out results_2049669.assoc.linear_clumped") results_2049669_clumped <- read.table("results_2049669.assoc.linear_clumped.clumped", header=T) results_2049669_clumped[1:15 ,1:6] ## 2 hits we have [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.