testGeneOverlap {GeneOverlap} | R Documentation |
Perform Fisher's exact test based on the information supplied in the GeneOverlap object, i.e. gene list A, B and genome size. This function also calculates the Jaccard index. Will set the tested Boolean label after done.
## S4 method for signature 'GeneOverlap' testGeneOverlap(object)
object |
A GeneOverlap object. |
A GeneOverlap object with valid p-value, odds ratio, Jaccard index and contingency table. The tested Boolean label is set to true. Use show or print to display a summary of the object. Use accessors to get information of each slot.
data(GeneOverlap) go.obj <- newGeneOverlap(hESC.ChIPSeq.list$H3K4me3, hESC.ChIPSeq.list$H3K27me3, genome.size=gs.RNASeq) go.obj <- testGeneOverlap(go.obj) getPval(go.obj) getOddsRatio(go.obj) getJaccard(go.obj) getContbl(go.obj) print(go.obj)