CollectionType {GSEABase}R Documentation

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(...)
ExpressionSetCollection(...)
ChrCollection(ids,...)
ChrlocCollection(ids,...)
KEGGCollection(ids,...)
MapCollection(ids,...)
OMIMCollection(ids,...)
PMIDCollection(ids,...)
PfamCollection(ids, ...)
PrositeCollection(ids, ...)
GOCollection(ids, evidenceCode="ANY", ...)
BroadCollection(category, subCategory=NA, ...)

Arguments

category (Required) Broad category, one of "c1" (postitional), "c2" (curated), "c3" (motif), "c4" (computational).
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).
... Additional arguments, usually none but see specific linkS4class{CollectionType} classes for possibilities.

Value

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

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

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=new("ScalarCharacter","c2"))
## change collectionType of gs2
gs2 <- gs1
collectionType(gs2) <- NullCollection()

[Package GSEABase version 1.0.3 Index]