#acl All:read DanieleMerico:write,delete,revert
= Fisher's Exact Test for Competitive Gene-set Enrichment =
== Outline ==
To run these functions you need:
 * a collection of gene-sets, in list format
 * the set of genes to be tested (i.e. "experimental genes"), in character format
 * the gene universe-set (e.g. all genes on your experimental platform)

Notes:
 * all sets are restricted to the universe within both functions
 * the FDR estimation takes quite a bit of time with 2000 iterations; efficiency suggestions welcome!
== Code ==
 * Function to generate FET p-values and other simple statistics <<BR>>
 [[attachment:Fisher_Enrichment_13.R]]
 * Function to empirically estimate FDR q-value (random generation of experimental gene-set)
 [[attachment:Fisher_Enrichment_FDR_13_1.R]]

{{{
#!rscript numbers=off

enr.df <- f.Enr_Fisher (
		GS.ls        = , # list, slot names = gene-set IDs, slot content = gene IDs 
 		GS_names.chv = , # character array, values = gene-set IDs, names = gene-set full names
 		exp.genes    = , # character array, values = experimental gene IDs 
 		uni.genes    =   # character array, values = all the genes in the platform
 		)

enr.df$FDR <- f.Fisher_FDR (
		GS.ls       = , # as above
		exp.genes   = , # as above
		uni.genes   = , # as above
		pval_obs.nv = enr.df$pvalue, 
		iter.n = , # numeric value (default 2000)
		)


}}}