GSEABase (version 1.28.0)

CollectionType: Collection Type Class Constructors

Description

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'.)

Usage

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, ...)

Arguments

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 CollectionType classes for possibilities.

Value

An object of the same class as the function name, initialized as appropriate for the collection.

See Also

CollectionType,

Examples

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"))