CollectionType-class {GSEABase} | R Documentation |
These classes provides a way to tag the origin of a
GeneSet
. 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
.)
The following classes can tag gene sets; GO, KEGG, Chr, Chrloc,
OMIM, and PMID
collections can be derived from chip or organism
‘annotation’ packages.
getBroadSets
,
toBroadXML
.ExpressionSet
. Usually
created during a call to GeneSet
or
GeneColorSet
.GOCollection
,
specifically from files described by the OBO file format. See
OBOCollection
Objects are instantiated with calls to CollectionType
constructors, with slot names as possible arguments.
CollectionType
classes (Null, ComputedCollection,
ExpressionSet
) have the slot:
type
:"ScalarCharacter"
containing the character string representation of this
CollectionType
.
CollectionIdType
classes (KEGG, OMIM, PMID, Chr, Chrloc,
Map, GO
) extend the CollectionType
and have the additional
slot:
ids
:"character"
containing a
vector of character string representations of corresponding
identifiers, e.g., ‘KEGG’ or ‘GO’ terms.
GOCollection
extends CollectionIdType
and has the
additional slot:
evidenceCode
:"character"
,
containing GO evidence codes used to construct the gene set.
OBOCollection
extends GOCollection
; see
OBOCollection
.
BroadCollection
has slots:
category
:"ScalarCharacter"
containing terms from the Broad list of categories, or NA
subCategory
:"ScalarCharacter"
containing Broad sub-categories, or NA
CollectionType
classes have methods:
signature(object = "GeneSet", value =
"CollectionType")
: Replace the CollectionType
signature(object = "CollectionType")
:
Retrieve the collection type.signature(e1="CollectionType",
e2="CollectionType")
: return e1
when class(e1)
and
class(e2)
are the same, or ComputedCollection
when different.signature(object = "CollectionType")
: display the
collection type.
CollectionIdType
classes inherit CollectionType
methods,
and have in addition:
signature(object="CollectionIdType")
: Retrieve the
identifiers of the collection type.signature(object="CollectionIdType", i="missing",
j="missing", ..., ids=ids(object))
: return a subset of
object
containing only ids in ids
signature(e1="CollectionIdType",
e2="CollectionIdType")
: always return ComputedCollection
.
GOCollection
inherits CollectionIdType
methods, and has
in addition:
GOENTREZID
.signature(object="CollectionIdType", i="missing",
j="missing", ..., evidenceCode=evidenceCode(object),
ontology=ontology(object))
: return a subset of
object
containing only evidence and ontology codes in
evidenceCode
, ontology
. This method passes
arguments ... to [,CollectionIdType
methods.
BroadCollection
has methods:
category
of the Broad
collection.Martin Morgan <mtmorgan@fhcrc.org>
CollectionType
consturctors.
names(getClass("CollectionType")@subclasses) ## Create a CollectionType and ask for its type collectionType(ExpressionSetCollection()) ## Not run: ## Read two GeneSets from a Broad XML file into a list, verify that ## they are both BroadCollection's. Category / subcategory information ## is unique to Broad collections. fl <- system.file("extdata", "Broad.xml", package="GSEABase") sets <- getBroadSets(fl) sapply(sets, collectionType) ## End(Not run) ## ExpressionSets are tagged with ExpressionSetCollection; there is no ## 'category' information. data(sample.ExpressionSet) gs <- GeneSet(sample.ExpressionSet[100:109], setName="sample.GeneSet", setIdentifier="123") collectionType(gs) ## GOCollections are created by reference to GO terms and evidenceCodes GOCollection("GO:0005488") ## requires library(GO); EntrezIdentifers automatically created ## Not run: GeneSet(GOCollection(c("GO:0005488", "GO:0019825"), evidenceCode="IDA")) ## End(Not run)