GeneOverlap (version 1.8.0)

getReadonly: Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class

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

## S3 method for class 'GeneOverlap':
getIntersection(object)
## S3 method for class 'GeneOverlap':
getUnion(object)
## S3 method for class 'GeneOverlap':
getTested(object)
## S3 method for class 'GeneOverlap':
getContbl(object)
## S3 method for class 'GeneOverlap':
getPval(object)
## S3 method for class 'GeneOverlap':
getOddsRatio(object)
## S3 method for class 'GeneOverlap':
getJaccard(object)

Arguments

object

A GeneOverlap object.

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.

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.

Examples

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)