Test and visualize gene overlaps

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Documentation for package ‘GeneOverlap’ version 1.34.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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