API for Bioconductor/GSEABase
Gene set enrichment data structures and methods

Global functions
$,GeneColorSet-method	Man page
$,GeneSet-method	Man page
&,ANY,GeneSetCollection-method	Man page
&,CollectionIdType,CollectionIdType-method	Man page
&,CollectionType,CollectionType-method	Man page
&,GeneColorSet,GeneColorSet-method	Man page
&,GeneColorSet,character-method	Man page
&,GeneSet,GeneSet-method	Man page
&,GeneSet,character-method	Man page
&,GeneSetCollection,ANY-method	Man page
&,GeneSetCollection,GeneSetCollection-method	Man page
.BroadXMLNodeToGeneSet_factory	Source code
.CollectionClasses	Source code
.GOFilterIds	Source code
.GO_slim	Source code
.GSC_CollectionIdTypes	Source code
.GSC_CollectionType	Source code
.GSC_ExpressionSet_helper	Source code
.GSC_GO_helper	Source code
.GSC_Pfam_helper	Source code
.GSC_filter_by_probe	Source code
.GSC_genes_helper	Source code
.GeneIdType_asString	Source code
.GeneSetToBroadXMLNode	Source code
.GeneSet_setters	Source code
.IdentifierClasses	Source code
.OBOids	Source code
.characterToIndex	Source code
.checkCode	Source code
.checkGOEvidenceCodes	Source code
.checkGOOntologyCode	Source code
.checkGeneColorSetLogicTypes	Source code
.checkGeneSetLogicTypes	Source code
.checkRequired	Source code
.collectionIdTypeLogic	Source code
.collectionTypeLogic	Source code
.collection_subset_chk	Source code
.colorConstructor	Source code
.constructors_GeneSet	Source code
.constructors_Simple	Source code
.fromOBO	Source code
.fromXML	Source code
.geneColorSetIntersect	Source code
.geneColorSetSetdiff	Source code
.geneColorSetUnion	Source code
.geneSetIntersect	Source code
.geneSetUnion	Source code
.getAnnMap	Source code
.getters	Source code
.glue	Source code
.incidence	Source code
.mapIdentifier_GCS_initialize	Source code
.mapIdentifiers_doRevMap	Source code
.mapIdentifiers_doWithMap	Source code
.mapIdentifiers_isMappable	Source code
.mapIdentifiers_isNullMap	Source code
.mapIdentifiers_map	Source code
.mapIdentifiers_normalize	Source code
.mapIdentifiers_revMap	Source code
.mapIdentifiers_selectMaps	Source code
.mapString	Source code
.mkFrameIdentifier	Source code
.nameAll	Source code
.requireQ	Source code
.setters	Source code
.showGeneColoring	Source code
.showGeneSet	Source code
.stopf	Source code
.subset	Source code
.subsetReplace	Source code
.toGmtRow	Source code
.toXML	Source code
.unique	Source code
.warningf	Source code
AnnoOrEntrezIdentifier	Man page Source code
AnnotationIdFactory	Source code
AnnotationIdentifier	Man page
AnnotationIdentifier-class	Man page
BroadCollection	Man page Source code
BroadCollection-class	Man page
ChrCollection	Man page
ChrCollection-class	Man page
ChrlocCollection	Man page
ChrlocCollection-class	Man page
CollectionIdType-class	Man page
CollectionType	Man page
CollectionType-class	Man page
ComputedCollection	Man page
ComputedCollection-class	Man page
ENSEMBLIdentifier	Man page
ENSEMBLIdentifier-class	Man page
EntrezIdentifier	Man page
EntrezIdentifier-class	Man page
EnzymeIdentifier	Man page
EnzymeIdentifier-class	Man page
ExpressionSetCollection	Man page
ExpressionSetCollection-class	Man page
GOAllFrameIdentifier	Man page Source code
GOAllFrameIdentifier-class	Man page
GOCollection	Man page Source code
GOCollection-class	Man page
GSEABase	Man page
GSEABase-package	Man page
GeneColorSet	Man page
GeneColorSet,BroadCollection-method	Man page
GeneColorSet,ExpressionSet-method	Man page
GeneColorSet,GOCollection-method	Man page
GeneColorSet,GeneIdentifierType-method	Man page
GeneColorSet,GeneSet-method	Man page
GeneColorSet,character-method	Man page
GeneColorSet,missing-method	Man page
GeneColorSet-class	Man page
GeneColorSet-methods	Man page
GeneIdentifierType	Man page
GeneIdentifierType-class	Man page
GeneSet	Man page
GeneSet,BroadCollection-method	Man page
GeneSet,ExpressionSet-method	Man page
GeneSet,GOCollection-method	Man page
GeneSet,GeneIdentifierType-method	Man page
GeneSet,character-method	Man page
GeneSet,missing-method	Man page
GeneSet-class	Man page
GeneSet-methods	Man page
GeneSetCollection	Man page
GeneSetCollection,ExpressionSet,missing,ChrlocCollection-method	Man page
GeneSetCollection,ExpressionSet,missing,CollectionIdType-method	Man page
GeneSetCollection,ExpressionSet,missing,CollectionType-method	Man page
GeneSetCollection,ExpressionSet,missing,GOCollection-method	Man page
GeneSetCollection,ExpressionSet,missing,KEGGCollection-method	Man page
GeneSetCollection,ExpressionSet,missing,PfamCollection-method	Man page
GeneSetCollection,ExpressionSet,missing,PrositeCollection-method	Man page
GeneSetCollection,GOAllFrame,missing,GOCollection-method	Man page
GeneSetCollection,GeneSet,missing,missing-method	Man page
GeneSetCollection,KEGGFrame,missing,KEGGCollection-method	Man page
GeneSetCollection,character,AnnotationIdentifier,ChrlocCollectio	Man page
GeneSetCollection,character,AnnotationIdentifier,CollectionIdTyp	Man page
GeneSetCollection,character,AnnotationIdentifier,CollectionType-	Man page
GeneSetCollection,character,AnnotationIdentifier,GOCollection-me	Man page
GeneSetCollection,character,AnnotationIdentifier,PfamCollection-	Man page
GeneSetCollection,character,AnnotationIdentifier,PrositeCollecti	Man page
GeneSetCollection,list,missing,missing-method	Man page
GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType-	Man page
GeneSetCollection,missing,AnnotationIdentifier,CollectionType-me	Man page
GeneSetCollection,missing,AnnotationIdentifier,GOCollection-meth	Man page
GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-me	Man page
GeneSetCollection-class	Man page
GeneSetCollection-methods	Man page
GenenameIdentifier	Man page
GenenameIdentifier-class	Man page
IdFactory	Source code
KEGGCollection	Man page
KEGGCollection-class	Man page
KEGGFrameIdentifier	Man page
KEGGFrameIdentifier-class	Man page
Logic,CollectionIdType,CollectionIdType-method	Man page
Logic,CollectionType,CollectionType-method	Man page
Logic,GeneSet,GeneSetCollection-method	Man page
Logic,character,GeneSet-method	Man page
Logic,character,GeneSetCollection-method	Man page
MapCollection	Man page
MapCollection-class	Man page
NullCollection	Man page
NullCollection-class	Man page
NullIdentifier	Man page
NullIdentifier-class	Man page
OBOCollection	Man page Source code
OBOCollection-class	Man page
OMIMCollection	Man page
OMIMCollection-class	Man page
PMIDCollection	Man page
PMIDCollection-class	Man page
PfamCollection	Man page
PfamCollection-class	Man page
PrositeCollection	Man page
PrositeCollection-class	Man page
RefseqIdentifier	Man page
RefseqIdentifier-class	Man page
SymbolIdentifier	Man page
SymbolIdentifier-class	Man page
UniprotIdentifier	Man page
UniprotIdentifier-class	Man page
[,CollectionIdType,missing,missing-method	Man page
[,ExpressionSet,GeneSet,ANY-method	Man page
[,GOCollection,missing,missing-method	Man page
[,GeneColorSet,character,ANY-method	Man page
[,GeneColorSet,numeric,ANY-method	Man page
[,GeneSet,character,ANY-method	Man page
[,GeneSet,numeric,ANY-method	Man page
[,GeneSetCollection,character,ANY-method	Man page
[,GeneSetCollection,logical,ANY-method	Man page
[,GeneSetCollection,numeric,ANY-method	Man page
[,OBOCollection,character,missing-method	Man page
[<-,GeneSetCollection,ANY,ANY,ANY-method	Man page
[<-,GeneSetCollection,ANY,ANY,GeneSet-method	Man page
[<-,GeneSetCollection,character,ANY,GeneSet-method	Man page
[[,GeneColorSet,character-method	Man page
[[,GeneColorSet,numeric-method	Man page
[[,GeneSet,character-method	Man page
[[,GeneSet,numeric-method	Man page
[[,GeneSetCollection,character-method	Man page
[[<-,GeneSetCollection,ANY,ANY,ANY-method	Man page
[[<-,GeneSetCollection,character,ANY,GeneSet-method	Man page
[[<-,GeneSetCollection,numeric,ANY,GeneSet-method	Man page
annotation,GeneIdentifierType-method	Man page
annotation<-,GeneIdentifierType,character-method	Man page
asBroadUri	Man page Source code
bcCategory	Man page
bcCategory,BroadCollection-method	Man page
bcSubCategory	Man page
bcSubCategory,BroadCollection-method	Man page
coerce,OBOCollection,graphNEL-method	Man page
coerce,graphNEL,OBOCollection-method	Man page
collectionType	Man page
collectionType,CollectionType-method	Man page
collectionType,GeneSet-method	Man page
collectionType<-	Man page
collectionType<-,GeneSet,CollectionType-method	Man page
coloring	Man page
coloring,GeneColorSet-method	Man page
coloring<-	Man page
coloring<-,GeneColorSet,data.frame-method	Man page
contributor	Man page
contributor,GeneSet-method	Man page
contributor<-	Man page
contributor<-,GeneSet,character-method	Man page
creationDate	Man page
creationDate,GeneSet-method	Man page
creationDate<-	Man page
creationDate<-,GeneSet,character-method	Man page
description,GeneSet-method	Man page
description<-,GeneSet,character-method	Man page
details	Man page
details,GeneColorSet-method	Man page
details,GeneSet-method	Man page
details-methods	Man page
evidenceCode	Man page
evidenceCode,GOCollection-method	Man page
geneColor	Man page
geneColor,GeneColorSet-method	Man page
geneColor<-	Man page
geneColor<-,GeneColorSet,factor-method	Man page
geneIdType	Man page
geneIdType,GeneIdentifierType-method	Man page
geneIdType,GeneSet-method	Man page
geneIdType<-	Man page
geneIdType<-,GeneSet,GeneIdentifierType-method	Man page
geneIdType<-,GeneSet,character-method	Man page
geneIds	Man page
geneIds,GeneSet-method	Man page
geneIds,GeneSetCollection-method	Man page
geneIds<-	Man page
geneIds<-,GeneSet,character-method	Man page
geneIds<-,GeneSetCollection,list-method	Man page
getBroadSets	Man page Source code
getGmt	Man page Source code
getOBOCollection	Man page Source code
goIds	Man page
goIds,GOCollection-method	Man page
goSlim	Man page
goSlim,ExpressionSet,GOCollection-method	Man page
goSlim,GOCollection,GOCollection-method	Man page
goSlim-methods	Man page
ids	Man page
ids,CollectionIdType-method	Man page
incidence	Man page
incidence,GeneSet-method	Man page
incidence,GeneSetCollection-method	Man page
incidence-methods	Man page
initialize,GeneColorSet-method	Man page
initialize,GeneIdentifierType-method	Man page
initialize,GeneSet-method	Man page
intersect,ANY,GeneSetCollection-method	Man page
intersect,CollectionIdType,CollectionIdType-method	Man page
intersect,CollectionType,CollectionType-method	Man page
intersect,GeneColorSet,GeneColorSet-method	Man page
intersect,GeneSet,GeneSet-method	Man page
intersect,GeneSetCollection,ANY-method	Man page
io	Man page
longDescription	Man page
longDescription,GeneSet-method	Man page
longDescription<-	Man page
longDescription<-,GeneSet,character-method	Man page
mapIdentifiers	Man page
mapIdentifiers,ANY,ANY,ANY-method	Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method	Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierTyp	Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-me	Man page
mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-metho	Man page
mapIdentifiers,GeneColorSet,NullIdentifier,GeneIdentifierType-me	Man page
mapIdentifiers,GeneSet,GeneIdentifierType,AnnDbBimap-method	Man page
mapIdentifiers,GeneSet,GeneIdentifierType,GeneIdentifierType-met	Man page
mapIdentifiers,GeneSet,GeneIdentifierType,NullIdentifier-method	Man page
mapIdentifiers,GeneSet,GeneIdentifierType,environment-method	Man page
mapIdentifiers,GeneSet,GeneIdentifierType,missing-method	Man page
mapIdentifiers,GeneSet,NullIdentifier,GeneIdentifierType-method	Man page
mapIdentifiers,GeneSetCollection,GeneIdentifierType,missing-meth	Man page
mapIdentifiers-methods	Man page
mkScalar	Source code
names,GeneSetCollection-method	Man page
ontology	Man page
ontology,GOCollection-method	Man page
organism	Man page
organism,GOAllFrameIdentifier-method	Man page
organism,GeneIdentifierType-method	Man page
organism,GeneSet-method	Man page
organism,KEGGFrameIdentifier-method	Man page
organism<-	Man page
organism<-,GeneSet,character-method	Man page
phenotype	Man page
phenotype,GeneColorSet-method	Man page
phenotype<-	Man page
phenotype<-,GeneColorSet,character-method	Man page
phenotypeColor	Man page
phenotypeColor,GeneColorSet-method	Man page
phenotypeColor<-	Man page
phenotypeColor<-,GeneColorSet,factor-method	Man page
pubMedIds,GeneSet-method	Man page
pubMedIds<-,GeneSet,character-method	Man page
setIdentifier	Man page
setIdentifier,GeneSet-method	Man page
setIdentifier<-	Man page
setIdentifier<-,GeneSet,character-method	Man page
setName	Man page
setName,GeneSet-method	Man page
setName<-	Man page
setName<-,GeneSet,character-method	Man page
setVersion	Man page
setVersion,GeneSet-method	Man page
setVersion<-	Man page
setVersion<-,GeneSet,Versions-method	Man page
setdiff,ANY,GeneSetCollection-method	Man page
setdiff,CollectionIdType,CollectionIdType-method	Man page
setdiff,CollectionType,CollectionType-method	Man page
setdiff,GeneColorSet,GeneColorSet-method	Man page
setdiff,GeneSet,GeneSet-method	Man page
setdiff,GeneSetCollection,ANY-method	Man page
show,AnnotationIdentifier-method	Man page
show,BroadCollection-method	Man page
show,CollectionIdType-method	Man page
show,CollectionType-method	Man page
show,GOCollection-method	Man page
show,GeneColorSet-method	Man page
show,GeneIdentifierType-method	Man page
show,GeneSet-method	Man page
show,GeneSetCollection-method	Man page
show,OBOCollection-method	Man page
subsets	Man page
subsets,OBOCollection-method	Man page
toBroadXML	Man page Source code
toGmt	Man page
toGmt,GeneSet-method	Man page
toGmt,GeneSetCollection-method	Man page
union,ANY,GeneSetCollection-method	Man page
union,CollectionIdType,CollectionIdType-method	Man page
union,CollectionType,CollectionType-method	Man page
union,GeneColorSet,GeneColorSet-method	Man page
union,GeneSet,GeneSet-method	Man page
union,GeneSetCollection,ANY-method	Man page
updateObject,GeneSetCollection-method	Man page
urls	Man page
urls,GeneSet-method	Man page
urls<-	Man page
urls<-,GeneSet,character-method	Man page
\|,ANY,GeneSetCollection-method	Man page
\|,CollectionIdType,CollectionIdType-method	Man page
\|,CollectionType,CollectionType-method	Man page
\|,GeneColorSet,GeneColorSet-method	Man page
\|,GeneColorSet,character-method	Man page
\|,GeneSet,GeneSet-method	Man page
\|,GeneSet,character-method	Man page
\|,GeneSetCollection,ANY-method	Man page
\|,GeneSetCollection,GeneSetCollection-method	Man page