These classes provides a way to tag the origin of a GeneSet. Collection types can be used in manipulating (e.g., selecting) sets, and can contain information specific to particular sets (e.g., category and subcategory classifications of BroadCollection.)
These functions construct collection types. Collection types can be used in manipulating (e.g., selecting) sets, and can contain information specific to particular sets (e.g., 'category' and 'subcategory' classifications of 'BroadCollection'.)
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). The GeneSet class provides a common data structure for representing gene sets. The GeneColorSet class allows genes in a set to be associated with phenotypes. The GeneSetCollection class facilitates grouping together a list of related gene sets. The GeneIdentifierType class hierarchy reflects how genes are represented (e.g., Entrez versus symbol) in the gene set. mapIdentifiers provides a way to convert identifiers in a set from one type to another. The CollectionType class hierarchy reflects how the gene set was made, and can order genes into distinct sets or collections.
A GeneColorSet extends GeneSet to allow genes to be 'colored'. Coloring means that for a particular phenotype, each gene has a color (e.g., expression levels "up", "down", or "unchanged") and a phenotypic consequence (e.g., the phenotype is "enhanced" or "reduced").
GeneColorSet
(Package: GSEABase) :
Methods to Construct "GeneColorSet" Instances
GeneColorSet is a generic for constructing gene color sets (i.e., gene sets with "coloring" to indicate how features of genes and phenotypes are associated).
This class provides a way to tag the meaning of gene symbols in a GeneSet. For instance, a GeneSet with gene names derived from a Bioconductor annotation package (e.g., via ExpressionSet) initially have a GeneIdentifierType of AnnotationIdentifier.
Gene identifier classes and functions are used to indicate what the list of genes in a gene set represents (e.g., Entrez gene identifiers are tagged with EntrezIdentifier(), Bioconductor annotations with AnnotationIdentifier()).
A GeneSet contains a set of gene identifiers. Each gene set has a geneIdType, indicating how the gene identifiers should be interpreted (e.g., as Entrez identifiers), and a collectionType, indicating the origin of the gene set (perhaps including additional information about the set, as in the BroadCollection type).
a GeneSetCollection is a collection of related GeneSets. The collection can mix and match different types of gene sets. Members of the collection are refered to by the setNames of each gene set.
providing 
.