Gene set enrichment data structures and methods
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Documentation for package ‘GSEABase’ version 1.60.0
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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 --
| 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" |