[R] FDR for hypergeometric tests

[darteta001 at ikasle.ehu.es]

Dear list,

I have performed several tests for the hypergeometric distribution 
using phyper() for some gene annotation categories as follows

>phyper(26,830,31042,337, lower.tail=F)
>phyper(16,387,31042,337, lower.tail=F)
 .
 .
 .

I am only running some selected categories but I would like to correct 
this value for multiple testing since I 
have 3121 possible tests according to 3121 annotation categories. I 
think that for 
the case of Bonferroni corrections, I should correct this output by 
the total number of possible tests conducted (3121):

>phyper(26,830,31042,337, lower.tail=F)*3121
>phyper(16,387,31042,337, lower.tail=F)*3121

But I would like to perform FDR, i.e. Benjamini correction. I know 
that multtest package has the function mt.rawp2adjp() but I would need 
to save all the p.values for the 3121 in a vector and use this as a 
parameter of 
the function. Is there another way of computing this adjusted p.value 
for only some of the categories?

Thanks for your help,

David

(R version 2.6.0)
(Windows OS)