Constructor for the GeneOverlap class

Description

Use this function to create objects of the GeneOverlap class.

Usage

1
2
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

1
2
3
4
5
6
7
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)