GeneSetCollection is a collection of related
GeneSets. The collection can mix and match
different types of gene sets. Members of the collection are refered to
by the setNames of each gene set.
GeneSetCollection with a
GeneSetCollection method, e.g., from a list of gene sets
or with several gene sets provided as argument to the constructor. See
examples below..Data:"list", containing the
gene sets."list", from data part.
Class "vector", by class "list", distance 2.
Class "AssayData", by class "list", distance 2.GeneSetCollection methods
and getBroadSets for convenient construction methods.length, ,
lapply also work on GeneSetCollection).
signature(object = "GeneSetCollection"):
return a list, with each member a character vector of gene
identifiers from the gene set collection.signature(object="GeneSetCollection",
value="list"): assign character vectors in value to
corresponding geneIds of object.signature(x = "GeneSetCollection"): return the
setName of each gene set in the colloection.signature(x = "GeneSetCollection", y = "ANY"),
signature(x = "ANY", y = "GeneSetCollection"): ...signature(e1 = "GeneSetCollection", e2 = "ANY"),
signautre(e1 = "GeneSet", e2 = "GeneSetCollection"),
signautre(e1 = "character", e2 = "GeneSetCollection"),
signature(e1 = "ANY", e2 = "GeneSetCollection"):
calculate the logical `or` (union) of all gene identifiers
in an object over all members of the gene set collection.signature(x = "GeneSetCollection", y = "ANY"),
signature(x = "ANY", y = "GeneSetCollection"): ...signature(e1 = "GeneSetCollection", e2 = "ANY"),
signautre(e1 = "character", e2 = "GeneSetCollection"),
signautre(e1 = "GeneSet", e2 = "GeneSetCollection"),
signature(e1 = "ANY", e2 = "GeneSetCollection"):
calculate the logical `and' (intersection) of all gene identifiers
in a gene set or character vector, over all members of the gene
set collection.signature(x = "GeneSetCollection", y = "ANY"):
calculate the logical set difference betwen all gene sets in a
collection and the gene identifiers of a gene set or character
vector. A setdiff method must be available for
x="GeneSet" and the type of y. signature(x = "GeneSetCollection", i = "ANY", j = "ANY",
value = "ANY"),
signature(x = "GeneSetCollection", i = "ANY", j = "ANY",
value = "GeneSet"),
signature(x = "GeneSetCollection", i = "character", j =
"ANY", value = "GeneSet"): assign new sets to existing set
members. To add entirely new sets, use a
GeneSetCollection constructor.
signature(x = "GeneSetCollection", i = "logical"),
signature(x = "GeneSetCollection", i = "numeric"),
signature(x = "GeneSetCollection", i = "character"): create
a GeneSetCollection consisting of a subset of the current
set. All indicies i must already be present in the set.
signature(x = "GeneSetCollection", i = "character"):
Select a single gene set from the collection. Methods for
i="numeric" are inherited from list.signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "ANY"),
signature(x = "GeneSetCollection", i = "numeric", j = "ANY", value = "GeneSet"),
signature(x = "GeneSetCollection", i = "character", j = "ANY", value = "GeneSet"):
Replace a gene set in the collecton with another.
value = "ANY" serves to stop invalid assignments.updateObject. Use updateObject
to update a GeneSetCollection and all contained
GeneSets to their current defintion.GeneIdentifierType to another. See
mapIdentifiers and specific methods in
GeneIdentifierType for additional detail.incidence-methods.toGmt.signature(object="GeneSetCollection"): provide a
compact representation of object.GeneSet, GeneColorSet.
gs1 <- GeneSet(setName="set1", setIdentifier="101")
gs2 <- GeneSet(setName="set2", setIdentifier="102")
## construct from indivdiual elements...
gsc <- GeneSetCollection(gs1, gs2)
## or from a list
gsc <- GeneSetCollection(list(gs1, gs2))
## 'names' are the setNames
names(gsc)
## a collection of a single gene set
gsc["set1"]
## a gene set
gsc[["set1"]]
## set names must be unique
try(GeneSetCollection(gs1, gs1))
try(gsc[c("set1", "set1")])
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