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

In GeneOverlap: Test and visualize gene overlaps

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

## 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

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)

Example output

[1] "ENSG00000187634" "ENSG00000188976" "ENSG00000187583" "ENSG00000188290"
[5] "ENSG00000188157" "ENSG00000131591"
[1] "ENSG00000187634" "ENSG00000188976" "ENSG00000187961" "ENSG00000187583"
[5] "ENSG00000187642" "ENSG00000188290"
[1] TRUE
     notA  inA
notB 7449 9894
inB   299 3554
[1] 0
[1] 8.948101
[1] 0.2585291

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