testGeneOverlap: Test function for the GeneOverlap class

In GeneOverlap: Test and visualize gene overlaps

Description

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.

Usage

## S4 method for signature 'GeneOverlap'
testGeneOverlap(object)

Arguments

object

A GeneOverlap object.

Value

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.

See Also

GeneOverlap-class

Examples

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)

GeneOverlap documentation built on Nov. 8, 2020, 5:46 p.m.