bootstrap method for enrichment analysis

bootstrapEnrichment.R

# http://ygc.name/2012/04/29/bootstrap-for-enrichment-analysis/

goboot <- cmpfun(function(goid,
                          sampleSize,
                          nboot=1000) {
    ratio <- rep(0, nboot)

    allgene <- unique(mappedkeys(org.Hs.egGO))
    allgeneInCategory <- unique(get(goid, org.Hs.egGO2ALLEGS))

    for (i in 1:nboot) {
        gene.sample <- sample(allgene, sampleSize)
        k <- sum(gene.sample %in% allgeneInCategory)
        ratio[i] <- k/sampleSize
    }
    return(ratio)
})

ratio <- goboot(goid="GO:0042221", sampleSize=100, nboot=1000)
## suppose a sample (100 genes) which have 35 genes annotated by GO:0042221
## the p value is:
pnorm(35/100, mean=mean(ratio), sd=sd(ratio), lower.tail=F)