testGeneOverlap: Test function for the GeneOverlap class

Description Usage Arguments Value See Also Examples

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

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## 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

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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 May 31, 2017, 2:35 p.m.