getGenomeSize: Accessors for the "genome.size" slot of the GeneOverlap class

In GeneOverlap: Test and visualize gene overlaps

Description

The genome.size slot contains the number of genes in the genome as an integer.

Usage

## S4 method for signature 'GeneOverlap'
getGenomeSize(object)
## S4 replacement method for signature 'GeneOverlap'
setGenomeSize(object) <- value

Arguments

object	A GeneOverlap object.
value	An integer representing genomic background.

Details

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

Value

An integer representing the genome size.

See Also

GeneOverlap-class

Examples

data(GeneOverlap)
go.obj <- newGeneOverlap(hESC.ChIPSeq.list$H3K27me3, 
                         hESC.RNASeq.list$"Exp Medium", 
                         genome.size=gs.RNASeq)
getGenomeSize(go.obj)
v.gs <- c(12e3, 14e3, 16e3, 18e3, 20e3)
setNames(sapply(v.gs, function(g) {
    setGenomeSize(go.obj) <- g
    go.obj <- testGeneOverlap(go.obj)
    getPval(go.obj)
}), v.gs)

Example output

[1] 21196
       12000        14000        16000        18000        20000 
1.000000e+00 9.999746e-01 6.039536e-05 9.006016e-24 5.589067e-51 

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