geneColor |
Class "GeneColorSet" |
geneColor,GeneColorSet-method |
Class "GeneColorSet" |
geneColor<-,GeneColorSet,factor-method |
Class "GeneColorSet" |
GeneColorSet |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,BroadCollection-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,character-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,ExpressionSet-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,GeneIdentifierType-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,GeneSet-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,GOCollection-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet,missing-method |
Methods to Construct "GeneColorSet" Instances |
GeneColorSet-class |
Class "GeneColorSet" |
GeneColorSet-methods |
Methods to Construct "GeneColorSet" Instances |
GeneIdentifierType |
Gene Identifier Class Constructors |
GeneIdentifierType-class |
Class "GeneIdentifierType" |
geneIds |
Class "GeneSet" |
geneIds,GeneSet-method |
Class "GeneSet" |
geneIds,GeneSetCollection-method |
Class "GeneSetCollection" |
geneIds<-,GeneSet,character-method |
Class "GeneSet" |
geneIds<-,GeneSetCollection,list-method |
Class "GeneSetCollection" |
geneIdType |
Class "GeneSet" |
geneIdType,GeneIdentifierType-method |
Class "GeneIdentifierType" |
geneIdType,GeneSet-method |
Class "GeneSet" |
geneIdType<-,GeneSet,character-method |
Class "GeneSet" |
geneIdType<-,GeneSet,GeneIdentifierType-method |
Class "GeneSet" |
GenenameIdentifier |
Gene Identifier Class Constructors |
GenenameIdentifier-class |
Class "GeneIdentifierType" |
GeneSet |
Methods to construct GeneSet instances |
GeneSet,BroadCollection-method |
Methods to construct GeneSet instances |
GeneSet,character-method |
Methods to construct GeneSet instances |
GeneSet,ExpressionSet-method |
Methods to construct GeneSet instances |
GeneSet,GeneIdentifierType-method |
Methods to construct GeneSet instances |
GeneSet,GOCollection-method |
Methods to construct GeneSet instances |
GeneSet,missing-method |
Methods to construct GeneSet instances |
GeneSet-class |
Class "GeneSet" |
GeneSet-methods |
Methods to construct GeneSet instances |
GeneSetCollection |
Methods to construct GeneSetCollection instances |
GeneSetCollection,character,AnnotationIdentifier,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,character,AnnotationIdentifier,CollectionType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,ExpressionSet,missing,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,ExpressionSet,missing,CollectionType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,ExpressionSet,missing,GOCollection-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,ExpressionSet,missing,KEGGCollection-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,GeneSet,missing,missing-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,list,missing,missing-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,missing,AnnotationIdentifier,CollectionIdType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,missing,AnnotationIdentifier,CollectionType-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,missing,AnnotationIdentifier,GOCollection-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection,missing,AnnotationIdentifier,KEGGCollection-method |
Methods to construct GeneSetCollection instances |
GeneSetCollection-class |
Class "GeneSetCollection" |
GeneSetCollection-methods |
Methods to construct GeneSetCollection instances |
getBroadSets |
Read and write gene sets from Broad or GMT formats |
getGmt |
Read and write gene sets from Broad or GMT formats |
getOBOCollection |
Read OBO-specified Gene Ontology Collections |
GOCollection |
Collection Type Class Constructors |
GOCollection-class |
Class "CollectionType" |
goIds |
Class "CollectionType" |
goIds,GOCollection-method |
Class "CollectionType" |
goSlim |
Methods for Function goSlim in Package ‘GSEABase’ |
goSlim,ExpressionSet,GOCollection-method |
Methods for Function goSlim in Package ‘GSEABase’ |
goSlim,GOCollection,GOCollection-method |
Methods for Function goSlim in Package ‘GSEABase’ |
goSlim-methods |
Methods for Function goSlim in Package ‘GSEABase’ |
GSEABase |
Gene set enrichment data structures and methods |
ids |
Class "CollectionType" |
ids,CollectionIdType-method |
Class "CollectionType" |
incidence |
Methods for Constructing Incidence Matricies Between GeneSets |
incidence,GeneSet-method |
Methods for Constructing Incidence Matricies Between GeneSets |
incidence,GeneSetCollection-method |
Methods for Constructing Incidence Matricies Between GeneSets |
incidence-methods |
Methods for Constructing Incidence Matricies Between GeneSets |
initialize,GeneColorSet-method |
Class "GeneColorSet" |
initialize,GeneIdentifierType-method |
Class "GeneIdentifierType" |
initialize,GeneSet-method |
Class "GeneSet" |
intersect,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
intersect,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
intersect,CollectionType,CollectionType-method |
Class "CollectionType" |
intersect,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
intersect,GeneSet,GeneSet-method |
Class "GeneSet" |
intersect,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
io |
Read and write gene sets from Broad or GMT formats |
MapCollection |
Collection Type Class Constructors |
MapCollection-class |
Class "CollectionType" |
mapIdentifiers |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,ANY,ANY,ANY-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneColorSet,GeneIdentifierType,AnnDbBimap-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneColorSet,GeneIdentifierType,environment-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneColorSet,GeneIdentifierType,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneColorSet,GeneIdentifierType,NullIdentifier-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneColorSet,NullIdentifier,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,GeneIdentifierType,AnnDbBimap-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,GeneIdentifierType,environment-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,GeneIdentifierType,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,GeneIdentifierType,missing-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,GeneIdentifierType,NullIdentifier-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSet,NullIdentifier,GeneIdentifierType-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers,GeneSetCollection,GeneIdentifierType,missing-method |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
mapIdentifiers-methods |
Methods for Function mapIdentifiers in Package ‘GSEABase’ |
setdiff,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
setdiff,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
setdiff,CollectionType,CollectionType-method |
Class "CollectionType" |
setdiff,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
setdiff,GeneSet,GeneSet-method |
Class "GeneSet" |
setdiff,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
setIdentifier |
Class "GeneSet" |
setIdentifier,GeneSet-method |
Class "GeneSet" |
setIdentifier<-,GeneSet,character-method |
Class "GeneSet" |
setName |
Class "GeneSet" |
setName,GeneSet-method |
Class "GeneSet" |
setName<-,GeneSet,character-method |
Class "GeneSet" |
setVersion |
Class "GeneSet" |
setVersion,GeneSet-method |
Class "GeneSet" |
setVersion<-,GeneSet,Versions-method |
Class "GeneSet" |
show,AnnotationIdentifier-method |
Class "GeneIdentifierType" |
show,BroadCollection-method |
Class "CollectionType" |
show,CollectionIdType-method |
Class "CollectionType" |
show,CollectionType-method |
Class "CollectionType" |
show,GeneColorSet-method |
Class "GeneColorSet" |
show,GeneIdentifierType-method |
Class "GeneIdentifierType" |
show,GeneSet-method |
Class "GeneSet" |
show,GeneSetCollection-method |
Class "GeneSetCollection" |
show,GOCollection-method |
Class "CollectionType" |
show,OBOCollection-method |
Class "OBOCollection" |
subsets |
Class "OBOCollection" |
subsets,OBOCollection-method |
Class "OBOCollection" |
SymbolIdentifier |
Gene Identifier Class Constructors |
SymbolIdentifier-class |
Class "GeneIdentifierType" |
[,CollectionIdType,missing,missing-method |
Class "CollectionType" |
[,ExpressionSet,GeneSet,ANY-method |
Class "GeneSet" |
[,GeneColorSet,character,ANY-method |
Class "GeneColorSet" |
[,GeneColorSet,numeric,ANY-method |
Class "GeneColorSet" |
[,GeneSet,character,ANY-method |
Class "GeneSet" |
[,GeneSet,numeric,ANY-method |
Class "GeneSet" |
[,GeneSetCollection,character,ANY-method |
Class "GeneSetCollection" |
[,GeneSetCollection,logical,ANY-method |
Class "GeneSetCollection" |
[,GeneSetCollection,numeric,ANY-method |
Class "GeneSetCollection" |
[,GOCollection,missing,missing-method |
Class "CollectionType" |
[,OBOCollection,character,missing-method |
Class "OBOCollection" |
[<-,GeneSetCollection,ANY,ANY,ANY-method |
Class "GeneSetCollection" |
[<-,GeneSetCollection,ANY,ANY,GeneSet-method |
Class "GeneSetCollection" |
[<-,GeneSetCollection,character,ANY,GeneSet-method |
Class "GeneSetCollection" |
[[,GeneColorSet,character-method |
Class "GeneColorSet" |
[[,GeneColorSet,numeric-method |
Class "GeneColorSet" |
[[,GeneSet,character-method |
Class "GeneSet" |
[[,GeneSet,numeric-method |
Class "GeneSet" |
[[,GeneSetCollection,character-method |
Class "GeneSetCollection" |
[[<-,GeneSetCollection,ANY,ANY,ANY-method |
Class "GeneSetCollection" |
[[<-,GeneSetCollection,character,ANY,GeneSet-method |
Class "GeneSetCollection" |
[[<-,GeneSetCollection,numeric,ANY,GeneSet-method |
Class "GeneSetCollection" |
|,ANY,GeneSetCollection-method |
Class "GeneSetCollection" |
|,CollectionIdType,CollectionIdType-method |
Class "CollectionType" |
|,CollectionType,CollectionType-method |
Class "CollectionType" |
|,GeneColorSet,character-method |
Class "GeneColorSet" |
|,GeneColorSet,GeneColorSet-method |
Class "GeneColorSet" |
|,GeneSet,character-method |
Class "GeneSet" |
|,GeneSet,GeneSet-method |
Class "GeneSet" |
|,GeneSetCollection,ANY-method |
Class "GeneSetCollection" |
|,GeneSetCollection,GeneSetCollection-method |
Class "GeneSetCollection" |