getList: Accessors for the "listA" and "listB" slots of GeneOverlap...

In GeneOverlap: Test and visualize gene overlaps

Description

The listA and listB slots hold the gene lists A and B as character vectors.

Usage

## S4 method for signature 'GeneOverlap'
getListA(object)
## S4 replacement method for signature 'GeneOverlap'
setListA(object) <- value
## S4 method for signature 'GeneOverlap'
getListB(object)
## S4 replacement method for signature 'GeneOverlap'
setListB(object) <- value

Arguments

object	A GeneOverlap object.
value	A character vector representing gene names.

Details

After setListX function is called, the tested Boolean label will be reset to false.

Value

A character vector representing gene list A/B.

See Also

GeneOverlap-class, newGeneOverlap

Examples

data(GeneOverlap)
go.obj <- newGeneOverlap(hESC.ChIPSeq.list$H3K4me3, 
                         hESC.ChIPSeq.list$H3K27me3, 
                         genome.size=gs.RNASeq)
go.obj <- testGeneOverlap(go.obj)
head(getListB(go.obj))
getTested(go.obj)  # true.
setListB(go.obj) <- hESC.ChIPSeq.list$H3K9me3
getTested(go.obj) # false.

Example output

[1] "ENSG00000187634" "ENSG00000188976" "ENSG00000187583" "ENSG00000188290"
[5] "ENSG00000188157" "ENSG00000237330"
[1] TRUE
[1] FALSE

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