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
Bioconductor/GSEABase documentation built on April 29, 2022, 12:04 p.m.