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), "c6"
(Oncogenic Pathway Activation Modules) "c7" (Immunologic
Signatures), "h" (Hallmark).
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.