bootstrap method for enrichment analysis
| # 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) |
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