| GeneIdentifierType-class {GSEABase} | R Documentation |
This class provides a way to tag the meaning of gene
symbols in a GeneSet. For instance, a GeneSet with gene
names derived from a Bioconductor annotation package (e.g., via
ExpressionSet) initially have a
GeneIdentifierType of AnnotationIdentifier.
The following classes are available, and derive from tables in ‘annotation’ packages
GeneIdentifierType.
All GeneIdentifierType classes have the following slot:
"ScalarCharacter"
containing the character string representation of this
GeneIdentifierType.
The AnnotationIdentifier class has an additional slot
"ScalarCharacter"
containing the name of the annotation package from which the
annotations (probe identifiers) are derived.
GeneIdentifierType classes are used in:
signature(type = "GeneIdentifierType"):
Create a new GeneSet using identifiers of
GeneIdentifierType.signature(type = "GeneIdentifierType"):
Create a new GeneColorSet using identifiers of
GeneIdentifierType.signature(object = "GeneSet", verbose=FALSE, value =
"GeneIdentifierType"): Changes the GeneIdentifierType of
object to value, attempting to convert symbols in
the process. This method calls mapIdentifiers(what=object,
to=value, from=geneIdType(what), verbose=verbose).signature(object = "GeneIdentifierType"):
return a character string representation of the type of this
object.signature(what="GeneSet", to="GeneIdentifierType"
from="missing", verbose=FALSE),
signature(what="GeneSet", to="GeneIdentifierType"
from="NullIdentifier", verbose=FALSE)
: See mapIdentifiers.signature(object = "GeneIdentifierType"): display
this object.
AnnotationIdentifier has the
following method:
signature(object = "AnnotationIdentifier"):
Retrieve the geneIdType (e.g., annotation string for
AnnotationIdentifier; ad hoc string for NullIdentifier).
AnnotationIdentifier classes are also used in:
signature(object = "AnnotationIdentifier"):
extract the name of the annotation package as a character string.signature(what = "GeneSet", to = "GeneIdentifierType", from
= "AnnotationIdentifier", verbose=FALSE),
signature(what = "GeneSet", to="AnnotationIdentifier", from
= "GeneIdentifierType", verbose=FALSE):
see mapIdentifiers.signature(object = "AnnotationIdentifier"):
Display object, including the annotation string if available.signature(.Object =
"AnnotationIdentifier"): Used internally during object creation.Martin Morgan <mtmorgan@fhcrc.org>
The example below lists GeneIdentifierType classes defined in
this package; See the help pages of these classes for specific information.
getSubclasses(getClass("GeneIdentifierType"))
# create an AnnotationIdentifier, and ask it's type
geneIdType(AnnotationIdentifier(annotation="hgu95av2"))
# Construct a GeneSet from an ExpressionSet, using the 'annotation'
# field of ExpressionSet to recognize the genes as AnnotationType
data(sample.ExpressionSet)
gs <- GeneSet(sample.ExpressionSet[100:109],
setName="sample.GeneSet", setIdentifier="123")
geneIdType(gs) # AnnotationIdentifier
## Read a Broad set from the system (or a url), and discover their
## GeneIdentifierType
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
bsets <- getBroadSets(fl)
sapply(bsets, geneIdType)
## try to combine gene sets with different set types
try(gs & sets[[1]])
## Not run:
## Use the annotation package associated with the original
## ExpressionSet to map to EntrezIdentifier() ...
geneIdType(gs) <- EntrezIdentifier()
...## and try again
gs & bsets[[1]]
## Another way to change annotation to Entrez (or other) ids
probeIds <- featureNames(sample.ExpressionSet)[100:109]
geneIds <- as.character(unlist(mget(probeIds, hgu95av2ENTREZID)))
GeneSet(EntrezIdentifier(),
setName="sample.GenSet2", setIdentifier="101",
geneIds=geneIds)
## End(Not run)
## Create a new identifier
setClass("FooIdentifier",
contains="GeneIdentifierType",
prototype=prototype(
type=new("ScalarCharacter", "Foo")))
## Create a constructor (optional)
FooIdentifier <- function() new("FooIdentifier")
geneIdType(FooIdentifier())
## tidy up
removeClass("FooIdentifier")