[R] how to create a plot of permutation of 30 random values and show proportion of values
David Winsemius
dw|n@em|u@ @end|ng |rom comc@@t@net
Fri Jan 24 12:12:35 CET 2020
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.anamarija using 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>
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