CollectionType {GSEABase} | R Documentation |
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'.)
NullCollection(...) ComputedCollection(...) ExpressionSetCollection(...) ChrCollection(ids,...) ChrlocCollection(ids,...) KEGGCollection(ids,...) MapCollection(ids,...) OMIMCollection(ids,...) PMIDCollection(ids,...) PfamCollection(ids, ...) PrositeCollection(ids, ...) GOCollection(ids=character(0), evidenceCode="ANY", ontology="ANY", ..., err=FALSE) OBOCollection(ids, evidenceCode="ANY", ontology="ANY", ...) BroadCollection(category, subCategory=NA, ...)
category |
(Required) Broad category, one of "c1" (postitional), "c2" (curated), "c3" (motif), "c4" (computational), "c5" (GO). |
subCategory |
(Optional) Sub-category; no controlled vocabulary. |
ids |
(Optional) Character vector of identifiers (e.g., GO, KEGG, or PMID terms). |
evidenceCode |
(Optional) Character vector of GO evidence codes to be included, or "ANY" (any identifier; the default). Evidence is a property of particular genes, rather than of the ontology, so evidenceCode is a convenient way of specifying how users of a GOCollection might restrict derived objects (as in done during create of a gene set from an expression set). |
ontology |
(Optional) Character vector of GO ontology terms to be included, or "ANY" (any identifier; the default). Unlike evidence code, ontology membership is enforced when GOCollection gene sets are constructed. |
err |
(Optional) logical scalar indicating whether non-existent
GO terms signal an error (TRUE ), or are silently ignored (FALSE ). |
... |
Additional arguments, usually none but see specific
linkS4class{CollectionType} classes for possibilities. |
An object of the same class as the function name, initialized as appropriate for the collection.
Martin Morgan <mtmorgan@fhcrc.org>
NullCollection() ## NullCollection when no collection type specified collectionType(GeneSet()) collectionType(GeneSet(collectionType=GOCollection())) ## fl could be a url fl <- system.file("extdata", "Broad.xml", package="GSEABase") gs1 <- getBroadSets(fl)[[1]] collectionType(gs1) # BroadCollection ## new BroadCollection, with different category bc <- BroadCollection(category="c2") ## change collectionType of gs2 gs2 <- gs1 collectionType(gs2) <- NullCollection() ## OBOCollection fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase") getOBOCollection(fl, evidenceCode="TAS") # returns OBOCollection OBOCollection(c("GO:0008967", "GO:0015119", "GO:0030372", "GO:0002732", "GO:0048090"))