Test and visualize gene overlaps


[Up] [Top]

Documentation for package ‘GeneOverlap’ version 1.34.0

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