Merge branch 'markziemann-master'

Author: assaron

vignettes/fgsea-tutorial.Rmd

@@ -157,3 +157,21 @@ And running fgsea:
 fgseaRes <- fgsea(pathways, ranks, minSize=15, maxSize=500)
 head(fgseaRes)
 ```
+
+## Over-representation test
+
+`fgsea` package also contains a function called `fora` for over-representation analysis based
+enrichment tests, based on the hypergeometric test.
+
+`fora` requires a foreground set of genes of interest, a background set consisting of all
+robustly detected genes, and some pathways.
+
+In the following example, the foreground (`fg`) consists of the 500 genes with the highest
+`stat` value.
+
+```{r}
+fg <-  names(head(exampleRanks[order(-exampleRanks)],500))
+bg <- names(exampleRanks)
+ora <- fora(genes=fg, universe=bg, pathways=examplePathways)
+head(ora)
+```