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
Fisher_Enrichment_13.R
Function to empirically estimate FDR q-value (random generation of experimental gene-set)
Fisher_Enrichment_FDR_13_1.R

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)
                )