getReadonly: Read-only accessors for the "intersection", "union",...

Description Usage Arguments Details Value Examples

Description

The intersection and union slots contain the gene names as character vectors. The is.tested slot contains a Boolean label indicating whether the object has been tested or not. The cont.tbl slot contains the contingency table as a matrix. The pval and odds.ratio slots contain the p-value and odds ratio as numerics, respectively. The Jaccard slot contains the Jaccard index as a numeric.

Usage

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## S4 method for signature 'GeneOverlap'
getIntersection(object)
## S4 method for signature 'GeneOverlap'
getUnion(object)
## S4 method for signature 'GeneOverlap'
getTested(object)
## S4 method for signature 'GeneOverlap'
getContbl(object)
## S4 method for signature 'GeneOverlap'
getPval(object)
## S4 method for signature 'GeneOverlap'
getOddsRatio(object)
## S4 method for signature 'GeneOverlap'
getJaccard(object)

Arguments

object

A GeneOverlap object.

Details

If the GeneOverlap object has not been tested yet, the returned Jaccard index, p-value and odds ratio will be NA, the contingency table will be an empty matrix.

Value

intersection

A character vector represents the overlapped genes.

union

A character vector represents the genes in the union of A and B.

is.tested

A Boolean represents whether the overlapping test has been performed or not.

cont.tbl

A matrix represents the contingency table.

pval

A numeric represents the significance of overlap.

odds.ratio

A numeric represents the odds ratio in comparison to the genomic background.

Jaccard

A numeric represents the Jaccard index between two sets.

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)
head(getIntersection(go.obj))
head(getUnion(go.obj))
getTested(go.obj)
getContbl(go.obj)
getPval(go.obj)
getOddsRatio(go.obj)
getJaccard(go.obj)

shenlab-sinai/geneoverlap-old documentation built on May 26, 2017, 8:06 a.m.