newGeneOverlap {GeneOverlap}R Documentation

Constructor for the GeneOverlap class

Description

Use this function to create objects of the GeneOverlap class.

Usage

newGeneOverlap(listA, listB, genome.size = NULL, 
    spec = c("mm9.gene", "hg19.gene", "rn4.gene"))

Arguments

listA

Gene list A. This should be a character vector or a factor.

listB

Gene list B. This should be a character vector or a factor.

genome.size

An integer represents the number of genes on the genome. If not specified, it will use the preset number based on "spec".

spec

A character string of the genome name. Currently choose one of: mm9.gene, hg19.gene, rn4.gene. The gene numbers are based on protein coding genes.

Value

A GeneOverlap object.

Note

Both listA and listB will be converted to unique character vectors before testing, that means, the duplicated gene names are removed and therefore not counted.

Examples

data(GeneOverlap)
go.obj <- newGeneOverlap(hESC.ChIPSeq.list$H3K4me3, 
                         hESC.ChIPSeq.list$H3K9me3, 
                         gs.RNASeq)
print(go.obj)  # not tested yet.
go.obj <- testGeneOverlap(go.obj)
print(go.obj)

[Package GeneOverlap version 1.30.0 Index]