R: Test and visualize gene overlaps

# Test and visualize gene overlaps

## Documentation for package ‘GeneOverlap’ version 1.48.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

GeneOverlap-package | Test and visualize overlaps between gene lists
drawHeatmap | Visualize GeneOverlapMatrix objects as heatmaps
drawHeatmap-method | Visualize GeneOverlapMatrix objects as heatmaps
GeneOverlap-class | Test overlap between two gene lists using Fisher's exact test.
GeneOverlapMatrix-class | Matrix representation of the pairwise overlaps between two gene sets
getContbl | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getContbl-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getGenomeSize | Accessors for the "genome.size" slot of the GeneOverlap class
getGenomeSize-method | Accessors for the "genome.size" slot of the GeneOverlap class
getGsetA | Read-only accessors for the various slots of the GeneOverlapMatrix class
getGsetA-method | Read-only accessors for the various slots of the GeneOverlapMatrix class
getGsetB | Read-only accessors for the various slots of the GeneOverlapMatrix class
getGsetB-method | Read-only accessors for the various slots of the GeneOverlapMatrix class
getIntersection | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getIntersection-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getJaccard | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getJaccard-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getListA | Accessors for the "listA" and "listB" slots of GeneOverlap class
getListA-method | Accessors for the "listA" and "listB" slots of GeneOverlap class
getListB | Accessors for the "listA" and "listB" slots of GeneOverlap class
getListB-method | Accessors for the "listA" and "listB" slots of GeneOverlap class
getMatrix | Read-only accessors for the various slots of the GeneOverlapMatrix class
getMatrix-method | Read-only accessors for the various slots of the GeneOverlapMatrix class
getNestedList | Read-only accessors for the various slots of the GeneOverlapMatrix class
getNestedList-method | Read-only accessors for the various slots of the GeneOverlapMatrix class
getOddsRatio | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getOddsRatio-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getPval | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getPval-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getSelfCompare | Read-only accessors for the various slots of the GeneOverlapMatrix class
getSelfCompare-method | Read-only accessors for the various slots of the GeneOverlapMatrix class
getTested | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getTested-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getUnion | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
getUnion-method | Read-only accessors for the "intersection", "union", "is.tested", "cont.tbl", "pval", "odds.ratio", "Jaccard" slots of the GeneOverlap class
gs.RNASeq | Genome size based on RNA-seq data
hESC.ChIPSeq.list | ChIP-seq gene lists
hESC.RNASeq.list | RNA-seq gene lists
newGeneOverlap | Constructor for the GeneOverlap class
newGOM | Constructor for the GeneOverlapMatrix class
print-method | Test overlap between two gene lists using Fisher's exact test.
print-method | Matrix representation of the pairwise overlaps between two gene sets
setGenomeSize<- | Accessors for the "genome.size" slot of the GeneOverlap class
setGenomeSize<--method | Accessors for the "genome.size" slot of the GeneOverlap class
setListA<- | Accessors for the "listA" and "listB" slots of GeneOverlap class
setListA<--method | Accessors for the "listA" and "listB" slots of GeneOverlap class
setListB<- | Accessors for the "listA" and "listB" slots of GeneOverlap class
setListB<--method | Accessors for the "listA" and "listB" slots of GeneOverlap class
show-method | Test overlap between two gene lists using Fisher's exact test.
show-method | Matrix representation of the pairwise overlaps between two gene sets
testGeneOverlap | Test function for the GeneOverlap class
testGeneOverlap-method | Test function for the GeneOverlap class
[ | Read-only accessors for the various slots of the GeneOverlapMatrix class
[-method | Read-only accessors for the various slots of the GeneOverlapMatrix class