newGeneOverlap: Constructor for the GeneOverlap class

In shenlab-sinai/geneoverlap-old: Test and visualize gene overlaps

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)

shenlab-sinai/geneoverlap-old documentation built on May 29, 2019, 9:22 p.m.