newGeneOverlap {GeneOverlap} | R Documentation |
Use this function to create objects of the GeneOverlap class.
newGeneOverlap(listA, listB, genome.size = NULL, spec = c("mm9.gene", "hg19.gene", "rn4.gene"))
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. |
A GeneOverlap object.
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.
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)