newGeneOverlap: Constructor for the GeneOverlap class

In GeneOverlap: 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)

Example output

Detailed information about this GeneOverlap object:
listA size=13448, e.g. ENSG00000187634 ENSG00000188976 ENSG00000187961
listB size=297, e.g. ENSG00000215912 ENSG00000232423 ENSG00000204501
Intersection size=253, e.g. ENSG00000215912 ENSG00000121903 ENSG00000157184
Union size=13492, e.g. ENSG00000187634 ENSG00000188976 ENSG00000187961
Genome size=21196
Overlap has not been tested yet. Use testGeneOverlap method.
Detailed information about this GeneOverlap object:
listA size=13448, e.g. ENSG00000187634 ENSG00000188976 ENSG00000187961
listB size=297, e.g. ENSG00000215912 ENSG00000232423 ENSG00000204501
Intersection size=253, e.g. ENSG00000215912 ENSG00000121903 ENSG00000157184
Union size=13492, e.g. ENSG00000187634 ENSG00000188976 ENSG00000187961
Genome size=21196
# Contingency Table:
     notA   inA
notB 7704 13195
inB    44   253
Overlapping p-value=4.6e-17
Odds ratio=3.4
Overlap tested using Fisher's exact test (alternative=greater)
Jaccard Index=0.0

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