CHANGES IN VERSION 1.21 ----------------------- SIGNIFICANT USER-VISIBLE CHANGES o GeneSetCollection,*,*,GOCollection-method respects evidenceCode and ontology CHANGES IN VERSION 1.19 ----------------------- NEW FEATURES o Added UniprotIdentifier class CHANGES IN VERSION 1.13 ----------------------- NEW FEATURES o Parse Broad gene set sub-categories. SIGNIFICANT USER-VISIBLE CHANGES o An ad-hoc identifier replaces the Ruuid-based one. CHANGES IN VERSION 1.5 ---------------------- SIGNIFICANT USER-VISIBLE CHANGES o Constructors for classes EntrezIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier can now accept an 'annotation' argument. This is used to indicate which annotation package the identifiers are from, e.g., EntrezIdentifier("hgu95av2.db") indicates that the EntrezId's are from the hgu95av2.db package. o GOCollection now tracks ontology as well as evidenceCode. o Add ComputedCollection class to describe gene set collections resulting from computations. o Additional GeneSetCollection constructors o Add OBOCollection class for reading OBO gene sets, including functions to retrieve OBO collections from the internet (getOBOCollectoin) and convert OBOCollections to and from graphNEL objects. o GeneSets constructed from GOCollections require a geneIdType with an appropriate (i.e., GO to identifier) mapping, e.g., geneIdType=EntrezIdentifier("org.Hs.eg.db") NEW FEATURES o geneIdType<- and mapIdentifiers can now map between any two identifier types within an annotation package, e.g., SymbolIdentifer('org.Hs.eg.db') to GenenameIdentifier('org.Hs.eg.db') o Parse revised Broad gene sets. o More extensive information in some 'show' methods o Added a mapIdentifiers method to allow maps with user-supplied AnnDbBimap objects BUG FIXES o GO evidenceCodes updated to current codes available as defined in GO o GeneSetCollection,ExpressionSet,(Pfam|Prosite|Chrloc)Collection-method now correctly navigate the underlying annotations and create gene set collections o A GeneSetCollection constructed with a named list could incorrectly propagate the set names. o Export MapCollection class o Mapping AnnotationIdentifer to AnnotationIdentifier failed due to incorrect method selection (start date: 9 February, 2008)