[R] Need help to calculate allele score

Bert Gunter bgunter@4567 @end|ng |rom gm@||@com
Wed Nov 25 22:51:10 CET 2020


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 <anasjamshed1994 using 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 using 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]]



More information about the R-help mailing list