This list has a no-homework policy. Referring to the posting guide linked below:
"*Basic statistics and classroom homework:* R-help is not intended for these." Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Nov 25, 2020 at 1:27 PM Anas Jamshed <anasjamshed1...@gmail.com> wrote: > 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. > [[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.
