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
AnnoOrEntrezIdentifier Man page Source code
AnnotationIdFactory Source code
AnnotationIdentifier Man page
AnnotationIdentifier-class Man page
BroadCollection Man page Source code
BroadCollection-class Man page
BroadXMLNodeToGeneSet_factory Source code
ChrCollection Man page
ChrCollection-class Man page
ChrlocCollection Man page
ChrlocCollection-class Man page
CollectionClasses Source code
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
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
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
GeneIdType_asString Source code
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
GeneSetToBroadXMLNode Source code
GeneSet_setters Source code
GenenameIdentifier Man page
GenenameIdentifier-class Man page
IdFactory Source code
IdentifierClasses Source code
KEGGCollection Man page
KEGGCollection-class Man page
KEGGFrameIdentifier Man page Source code
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
OBOids Source code
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
UnigeneIdentifier Man page
UnigeneIdentifier-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
characterToIndex Source code
checkCode Source code
checkGOEvidenceCodes Source code
checkGOOntologyCode Source code
checkGeneColorSetLogicTypes Source code
checkGeneSetLogicTypes Source code
checkRequired Source code
coerce,OBOCollection,graphNEL-method Man page
coerce,graphNEL,OBOCollection-method Man page
collectionIdTypeLogic Source code
collectionType Man page
collectionType,CollectionType-method Man page
collectionType,GeneSet-method Man page
collectionType<- Man page
collectionType<-,GeneSet,CollectionType-method Man page
collectionTypeLogic Source code
collection_subset_chk Source code
colorConstructor Source code
coloring Man page
coloring,GeneColorSet-method Man page
coloring<- Man page
coloring<-,GeneColorSet,data.frame-method Man page
constructors_GeneSet Source code
constructors_Simple Source code
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
fromOBO Source code
fromXML Source code
geneColor Man page
geneColor,GeneColorSet-method Man page
geneColor<- Man page
geneColor<-,GeneColorSet,factor-method Man page
geneColorSetIntersect Source code
geneColorSetSetdiff Source code
geneColorSetUnion Source code
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
geneSetIntersect Source code
geneSetUnion Source code
getAnnMap Source code
getBroadSets Man page Source code
getGmt Man page Source code
getOBOCollection Man page Source code
getters Source code
glue 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
mapIdentifier_GCS_initialize Source code
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
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
mkScalar Source code
nameAll Source code
names,GeneSetCollection-method Man page
ncidence Source code
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
requireQ Source code
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
setters Source code
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
showGeneColoring Source code
showGeneSet Source code
stopf Source code
subset Source code
subsetReplace Source code
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
toGmtRow Source code
toXML Source code
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
unique Source code
updateObject,GeneSetCollection-method Man page
urls Man page
urls,GeneSet-method Man page
urls<- Man page
urls<-,GeneSet,character-method Man page
warningf Source code
|,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 Oct. 14, 2017, 7:01 a.m.