# Gene set enrichment data structures and methods

## Documentation for package ‘GSEABase’ version 1.40.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

GSEABase-package | Gene set enrichment data structures and methods

## -- A --

AnnoOrEntrezIdentifier | Gene Identifier Class Constructors
annotation-method | Class "GeneIdentifierType"
annotation<--method | Class "GeneIdentifierType"
AnnotationIdentifier | Gene Identifier Class Constructors
AnnotationIdentifier-class | Class "GeneIdentifierType"
asBroadUri | Read and write gene sets from Broad or GMT formats

## -- B --

bcCategory | Class "CollectionType"
bcCategory-method | Class "CollectionType"
bcSubCategory | Class "CollectionType"
bcSubCategory-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"
coerce-method | Class "OBOCollection"
CollectionIdType-class | Class "CollectionType"
CollectionType | Collection Type Class Constructors
collectionType | Class "GeneSet"
CollectionType-class | Class "CollectionType"
collectionType-method | Class "CollectionType"
collectionType-method | Class "GeneSet"
collectionType<- | Class "GeneSet"
collectionType<--method | Class "GeneSet"
coloring | Class "GeneColorSet"
coloring-method | Class "GeneColorSet"
coloring<- | Class "GeneColorSet"
coloring<--method | Class "GeneColorSet"
ComputedCollection | Collection Type Class Constructors
ComputedCollection-class | Class "CollectionType"
contributor | Class "GeneSet"
contributor-method | Class "GeneSet"
contributor<- | Class "GeneSet"
contributor<--method | Class "GeneSet"
creationDate | Class "GeneSet"
creationDate-method | Class "GeneSet"
creationDate<- | Class "GeneSet"
creationDate<--method | Class "GeneSet"

## -- D --

description-method | Class "GeneSet"
description<--method | Class "GeneSet"
details | Methods for Displaying Detailed GeneSet Information
details-method | Methods for Displaying Detailed GeneSet Information
details-methods | Methods for Displaying Detailed GeneSet Information

## -- E --

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

## -- G --

geneColor | Class "GeneColorSet"
geneColor-method | Class "GeneColorSet"
geneColor<- | Class "GeneColorSet"
geneColor<--method | Class "GeneColorSet"
GeneColorSet | Methods to Construct "GeneColorSet" Instances
GeneColorSet-class | Class "GeneColorSet"
GeneColorSet-method | Methods to Construct "GeneColorSet" Instances
GeneColorSet-methods | Methods to Construct "GeneColorSet" Instances
GeneIdentifierType | Gene Identifier Class Constructors
GeneIdentifierType-class | Class "GeneIdentifierType"
geneIds | Class "GeneSet"
geneIds-method | Class "GeneSet"
geneIds-method | Class "GeneSetCollection"
geneIds<- | Class "GeneSet"
geneIds<--method | Class "GeneSet"
geneIds<--method | Class "GeneSetCollection"
geneIdType | Class "GeneSet"
geneIdType-method | Class "GeneIdentifierType"
geneIdType-method | Class "GeneSet"
geneIdType<- | Class "GeneSet"
geneIdType<--method | Class "GeneSet"
GenenameIdentifier | Gene Identifier Class Constructors
GenenameIdentifier-class | Class "GeneIdentifierType"
GeneSet | Methods to construct GeneSet instances
GeneSet-class | Class "GeneSet"
GeneSet-method | Methods to construct GeneSet instances
GeneSet-methods | Methods to construct GeneSet instances
GeneSetCollection | Methods to construct GeneSetCollection instances
GeneSetCollection-class | Class "GeneSetCollection"
GeneSetCollection-method | Methods to construct GeneSetCollection instances
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
GOAllFrameIdentifier | Gene Identifier Class Constructors
GOAllFrameIdentifier-class | Class "GeneIdentifierType"
GOCollection | Collection Type Class Constructors
GOCollection-class | Class "CollectionType"
goIds | Class "CollectionType"
goIds-method | Class "CollectionType"
goSlim | Methods for Function goSlim in Package 'GSEABase'
goSlim-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

## -- I --

ids | Class "CollectionType"
ids-method | Class "CollectionType"
incidence | Methods for Constructing Incidence Matricies Between GeneSets
incidence-method | Methods for Constructing Incidence Matricies Between GeneSets
incidence-methods | Methods for Constructing Incidence Matricies Between GeneSets
initialize-method | Class "GeneColorSet"
initialize-method | Class "GeneIdentifierType"
initialize-method | Class "GeneSet"
intersect-method | Class "CollectionType"
intersect-method | Class "GeneColorSet"
intersect-method | Class "GeneSet"
intersect-method | Class "GeneSetCollection"
io | Read and write gene sets from Broad or GMT formats

## -- K --

KEGGCollection | Collection Type Class Constructors
KEGGCollection-class | Class "CollectionType"
KEGGFrameIdentifier | Gene Identifier Class Constructors
KEGGFrameIdentifier-class | Class "GeneIdentifierType"

## -- L --

Logic-method | Class "CollectionType"
Logic-method | Class "GeneSet"
Logic-method | Class "GeneSetCollection"
longDescription | Class "GeneSet"
longDescription-method | Class "GeneSet"
longDescription<- | Class "GeneSet"
longDescription<--method | Class "GeneSet"

## -- M --

MapCollection | Collection Type Class Constructors
MapCollection-class | Class "CollectionType"
mapIdentifiers | Methods for Function mapIdentifiers in Package 'GSEABase'
mapIdentifiers-method | Methods for Function mapIdentifiers in Package 'GSEABase'
mapIdentifiers-methods | Methods for Function mapIdentifiers in Package 'GSEABase'

## -- N --

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

## -- O --

OBOCollection | Collection Type Class Constructors
OBOCollection-class | Class "OBOCollection"
OMIMCollection | Collection Type Class Constructors
OMIMCollection-class | Class "CollectionType"
ontology | Class "CollectionType"
ontology-method | Class "CollectionType"
organism | Class "GeneSet"
organism-method | Class "GeneSet"
organism<- | Class "GeneSet"
organism<--method | Class "GeneSet"

## -- P --

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

## -- R --

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

## -- S --

setdiff-method | Class "CollectionType"
setdiff-method | Class "GeneColorSet"
setdiff-method | Class "GeneSet"
setdiff-method | Class "GeneSetCollection"
setIdentifier | Class "GeneSet"
setIdentifier-method | Class "GeneSet"
setIdentifier<- | Class "GeneSet"
setIdentifier<--method | Class "GeneSet"
setName | Class "GeneSet"
setName-method | Class "GeneSet"
setName<- | Class "GeneSet"
setName<--method | Class "GeneSet"
setVersion | Class "GeneSet"
setVersion-method | Class "GeneSet"
setVersion<- | Class "GeneSet"
setVersion<--method | Class "GeneSet"
show-method | Class "CollectionType"
show-method | Class "GeneColorSet"
show-method | Class "GeneIdentifierType"
show-method | Class "GeneSet"
show-method | Class "GeneSetCollection"
show-method | Class "OBOCollection"
subsets | Class "OBOCollection"
subsets-method | Class "OBOCollection"
SymbolIdentifier | Gene Identifier Class Constructors
SymbolIdentifier-class | Class "GeneIdentifierType"

## -- T --

toBroadXML | Read and write gene sets from Broad or GMT formats
toGmt | Read and write gene sets from Broad or GMT formats
toGmt-method | Class "GeneSet"
toGmt-method | Class "GeneSetCollection"

## -- U --

UnigeneIdentifier | Gene Identifier Class Constructors
UnigeneIdentifier-class | Class "GeneIdentifierType"
union-method | Class "CollectionType"
union-method | Class "GeneColorSet"
union-method | Class "GeneSet"
union-method | Class "GeneSetCollection"
UniprotIdentifier | Gene Identifier Class Constructors
UniprotIdentifier-class | Class "GeneIdentifierType"
updateObject-method | Class "GeneSetCollection"
urls | Class "GeneSet"
urls-method | Class "GeneSet"
urls<- | Class "GeneSet"
urls<--method | Class "GeneSet"

## -- misc --

$-method | Class "GeneColorSet"
$-method | Class "GeneSet"
&-method | Class "CollectionType"
&-method | Class "GeneColorSet"
&-method | Class "GeneSet"
&-method | Class "GeneSetCollection"
[-method | Class "CollectionType"
[-method | Class "GeneColorSet"
[-method | Class "GeneSet"
[-method | Class "GeneSetCollection"
[-method | Class "OBOCollection"
[<--method | Class "GeneSetCollection"
[[-method | Class "GeneColorSet"
[[-method | Class "GeneSet"
[[-method | Class "GeneSetCollection"
[[<--method | Class "GeneSetCollection"
|-method | Class "CollectionType"
|-method | Class "GeneColorSet"
|-method | Class "GeneSet"
|-method | Class "GeneSetCollection"