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 |