[R] Need help to calculate allele score

[Anas Jamshed]

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

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