| GeneSet {GSEABase} | R Documentation |
Use GeneSet to construct gene sets from ExpressionSet,
character vector, or other objects.
GeneSet(type, ..., setIdentifier=.uniqueIdentifier())
type |
An argument determining how the gene set will be created, as described in the Methods section. |
setIdentifier |
A ScalarCharacter or length-1 character
vector uniquely identifying the set. The default attempts to use
Ruuid to generate a unique identifier, or if Ruuid is
not avaiable assigns NA. |
... |
Additional arguments for gene set construction.
Methods have required arguments, as outlined below; additional
arguments correspond to slot names GeneSet. |
signature(type = "missing", ...,
setIdentifier=.uniqueIdentifier())signature(type = "character", ...,
setIdentifier=.uniqueIdentifier())type.signature(type = "GeneIdentifierType", ...,
setIdentifier=.uniqueIdentifier())geneIdType
created from the GeneIdentifierType of type.signature(type = "ExpressionSet", ...,
setIdentifier=.uniqueIdentifier())ExpressionSet. geneIdType
is set to AnnotationIdentifier; the annotation field and
annotation package of the ExpressionSet are consulted to
determine organism, if possible. Short and long
descriptions from the ExpressionSet experimentData
title and abstract; pub med ids, urls, and contributor are also
derived from experimentData.signature(type = "GOCollection", ...,
geneIdType = EntrezIdentifier(),
setIdentifier=.uniqueIdentifier())type to
create a GeneSet . The default geneIdType assumes
that the identifiers are Entrez ids.signature(type = "BroadCollection", ..., urls = character(0),
setIdentifier=.uniqueIdentifier())urls to create a gene set. The url can be a local file or
internet connection, but must contain just a single gene set. See
getBroadSets for details.
GeneSet-class
GeneColorSet-class
## Empty gene set
GeneSet()
## Gene set from ExpressionSet
data(sample.ExpressionSet)
gs1 <- GeneSet(sample.ExpressionSet[100:109])
## GeneSet from Broad XML; 'fl' could be a url
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gs2 <- getBroadSets(fl)[[1]] # actually, a list of two gene sets
## GeneSet from list of gene identifiers
geneIds <- geneIds(gs2) # any character vector would do
gs3 <- GeneSet(geneIds)
## unspecified set type, so...
is(geneIdType(gs3), "NullIdentifier") == TRUE
## update set type to match encoding of identifiers
geneIdType(gs2)
geneIdType(gs3) <- EntrezIdentifier()
## other ways of accomplishing the same
gs4 <- GeneSet(geneIds, geneIdType=EntrezIdentifier())
gs5 <- GeneSet(EntrezIdentifier(), geneIds=geneIds)