It appears you are not trying to do this within individual SNPs. If I’m wrong then this would need to be done within a grouping procedure. And I’m not at all confident that you can estimate FDRs in this manner, but if your strategy is valid, then some variant of this untested code:
replicate ( 50, my.50.vals = { p.adjust(dfrm[ sample(1:3859763, 30), 2], method =‘BH’)}) It would be better in the future to make a small example that supports testing. David. Sent from my iPhone > On Jan 24, 2020, at 4:10 AM, Ana Marija <sokovic.anamar...@gmail.com> wrote: > > Hello, > > I have a data frame which looks like this: > >> head(a,20) > rs pvalue > 1: rs185642176 0.267407 > 2: rs184120752 0.787681 > 3: rs10904045 0.508162 > 4: rs35849539 0.875910 > 5: rs141633513 0.787759 > 6: rs4468273 0.542171 > 7: rs4567378 0.539484 > 8: rs7084251 0.126445 > 9: rs181605000 0.787838 > 10: rs12255619 0.192719 > 11: rs140367257 0.788008 > 12: rs10904178 0.969814 > 13: rs7918960 0.436341 > 14: rs61688896 0.526256 > 15: rs151283848 0.787284 > 16: rs140174295 0.989107 > 17: rs145945079 0.787015 > 18: rs4881370 0.455089 > 19: rs183895035 0.787015 > 20: rs181749526 0.787015 >> dim(a) > [1] 3859763 2 > > What I would like to do is to take random subsets of 30 of those rs > throughout the dataframe and find out which subsets of those generated > have FDR value <0.05 > > FDR I would calculate I guess with: > a$fdr=p.adjust(a$pvalue,method="BH") > > but I also guess I would be calculating only FDR for a particular > subset of 30 randomly chosen rs, not for the whole data set. > > The result I would like to present like in the attached plot. The > x-axis say proportion of SNPs and in my case SNP is equivalent to rs > > Can you please help with this, I really don't have idea how to go about this. > > Thanks > Ana > <Screen Shot 2020-01-23 at 2.09.26 PM.png> > ______________________________________________ > 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. ______________________________________________ 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.