Gene set enrichment data structures and methods


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Documentation for package ‘GSEABase’ version 1.0.3

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A B C D E G I K L M N O P R S T U X misc

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GSEABase-package Gene set enrichment data structures and methods

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$,GeneColorSet-method Class "GeneColorSet"
$,GeneSet-method Class "GeneSet"
&,ANY,GeneSetCollection-method Class "GeneSetCollection"
&,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"

-- A --

annotation,AnnotationIdentifier-method Class "GeneIdentifierType"
AnnotationIdentifier Gene Identifier Class Constructors
AnnotationIdentifier-class Class "GeneIdentifierType"
asBroadUri Read and Write XML Gene Sets

-- B --

bcCategory Class "CollectionType"
bcCategory,BroadCollection-method Class "CollectionType"
bcSubCategory Class "CollectionType"
bcSubCategory,BroadCollection-method Class "CollectionType"
BroadCollection Collection Type Class Constructors
BroadCollection-class Class "CollectionType"

-- C --

ChrCollection Collection Type Class Constructors
ChrCollection-class Class "CollectionType"
ChrlocCollection Collection Type Class Constructors
ChrlocCollection-class Class "CollectionType"
CollectionIdType-class Class "CollectionType"
CollectionType Collection Type Class Constructors
collectionType Class "GeneSet"
collectionType,CollectionType-method Class "CollectionType"
collectionType,GeneSet-method Class "GeneSet"
CollectionType-class Class "CollectionType"
collectionType<-,GeneSet,CollectionType-method Class "GeneSet"
coloring Class "GeneColorSet"
coloring,GeneColorSet-method Class "GeneColorSet"
coloring<-,GeneColorSet,data.frame-method Class "GeneColorSet"
contributor Class "GeneSet"
contributor,GeneSet-method Class "GeneSet"
contributor<-,GeneSet,character-method Class "GeneSet"
creationDate Class "GeneSet"
creationDate,GeneSet-method Class "GeneSet"
creationDate<-,GeneSet,character-method Class "GeneSet"

-- D --

description,GeneSet-method Class "GeneSet"
description<-,GeneSet,character-method Class "GeneSet"
details Methods for Displaying Detailed GeneSet Information
details,GeneColorSet-method Methods for Displaying Detailed GeneSet Information
details,GeneSet-method Methods for Displaying Detailed GeneSet Information
details-methods Methods for Displaying Detailed GeneSet Information

-- E --

EntrezIdentifier Gene Identifier Class Constructors
EntrezIdentifier-class Class "GeneIdentifierType"
EnzymeIdentifier Gene Identifier Class Constructors
EnzymeIdentifier-class Class "GeneIdentifierType"
evidenceCode Class "CollectionType"
evidenceCode,GOCollection-method Class "CollectionType"
ExpressionSetCollection Collection Type Class Constructors
ExpressionSetCollection-class Class "CollectionType"

-- G --

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,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 XML Gene Sets
GOCollection Collection Type Class Constructors
GOCollection-class Class "CollectionType"
goIds Class "CollectionType"
goIds,GOCollection-method Class "CollectionType"
GSEABase Gene set enrichment data structures and methods

-- I --

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,AnnotationIdentifier-method Class "GeneIdentifierType"
initialize,GeneColorSet-method Class "GeneColorSet"
initialize,GeneSet-method Class "GeneSet"
intersect,ANY,GeneSetCollection-method Class "GeneSetCollection"
intersect,GeneColorSet,GeneColorSet-method Class "GeneColorSet"
intersect,GeneSet,GeneSet-method Class "GeneSet"
intersect,GeneSetCollection,ANY-method Class "GeneSetCollection"

-- K --

KEGGCollection Collection Type Class Constructors
KEGGCollection-class Class "CollectionType"

-- L --

longDescription Class "GeneSet"
longDescription,GeneSet-method Class "GeneSet"
longDescription<-,GeneSet,character-method Class "GeneSet"

-- M --

MapCollection Collection Type Class Constructors
mapIdentifiers Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers,ANY,ANY,ANY-method Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers,GeneSet,AnnotationIdentifier,GeneIdentifierType-method Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers,GeneSet,AnnotationIdentifier,NullIdentifier-method Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers,GeneSet,GeneIdentifierType,AnnotationIdentifier-method Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers,GeneSet,GeneIdentifierType,environment-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,GeneSetCollection,GeneIdentifierType,missing-method Methods for Function mapIdentifiers in Package ‘GSEABase’
mapIdentifiers-methods Methods for Function mapIdentifiers in Package ‘GSEABase’

-- N --

names,GeneSetCollection-method Class "GeneSetCollection"
NullCollection Collection Type Class Constructors
NullCollection-class Class "CollectionType"
NullIdentifier Gene Identifier Class Constructors
NullIdentifier-class Class "GeneIdentifierType"

-- O --

OMIMCollection Collection Type Class Constructors
OMIMCollection-class Class "CollectionType"
organism Class "GeneSet"
organism,GeneSet-method Class "GeneSet"
organism<-,GeneSet,character-method Class "GeneSet"

-- P --

PfamCollection Collection Type Class Constructors
PfamCollection-class Class "CollectionType"
phenotype Class "GeneColorSet"
phenotype,GeneColorSet-method Class "GeneColorSet"
phenotype<-,GeneColorSet,character-method Class "GeneColorSet"
phenotypeColor Class "GeneColorSet"
phenotypeColor,GeneColorSet-method Class "GeneColorSet"
phenotypeColor<-,GeneColorSet,factor-method Class "GeneColorSet"
PMIDCollection Collection Type Class Constructors
PMIDCollection-class Class "CollectionType"
PrositeCollection Collection Type Class Constructors
PrositeCollection-class Class "CollectionType"
pubMedIds,GeneSet-method Class "GeneSet"
pubMedIds<-,GeneSet,character-method Class "GeneSet"

-- R --

RefseqIdentifier Gene Identifier Class Constructors
RefseqIdentifier-class Class "GeneIdentifierType"

-- S --

setdiff,ANY,GeneSetCollection-method Class "GeneSetCollection"
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"
SymbolIdentifier Gene Identifier Class Constructors
SymbolIdentifier-class Class "GeneIdentifierType"

-- T --

toBroadXML Read and Write XML Gene Sets

-- U --

UnigeneIdentifier Gene Identifier Class Constructors
UnigeneIdentifier-class Class "GeneIdentifierType"
union,ANY,GeneSetCollection-method Class "GeneSetCollection"
union,GeneColorSet,GeneColorSet-method Class "GeneColorSet"
union,GeneSet,GeneSet-method Class "GeneSet"
union,GeneSetCollection,ANY-method Class "GeneSetCollection"
urls Class "GeneSet"
urls,GeneSet-method Class "GeneSet"
urls<-,GeneSet,character-method Class "GeneSet"

-- X --

xml Read and Write XML Gene Sets

-- misc --

[,ExpressionSet,GeneSet-method Class "GeneSet"
[,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,logical-method Class "GeneSetCollection"
[,GeneSetCollection,numeric-method Class "GeneSetCollection"
[<-,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"
|,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"