getReadonly: Read-only accessors for the "intersection", "union",...
In shenlab-sinai/geneoverlap-old: Test and visualize gene overlaps

Description Usage Arguments Details Value Examples

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.

## 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)

object

A GeneOverlap object.

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.

`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.

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)