GeneSetCollection-class: Class "GeneSetCollection"
In GSEABase: Gene set enrichment data structures and methods

Description Objects from the Class Slots Extends Methods Author(s) See Also Examples

a 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.

Construct a 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:: Object of class "list", containing the gene sets.

Class "list", from data part. Class "vector", by class "list", distance 2. Class "AssayData", by class "list", distance 2.

Gene set collection construction

GeneSetCollection: See GeneSetCollection methods and getBroadSets for convenient construction methods.

Collection access (operations on lists, such as length, , lapply also work on GeneSetCollection).

geneIds: signature(object = "GeneSetCollection"): return a list, with each member a character vector of gene identifiers from the gene set collection.
geneIds<-: signature(object="GeneSetCollection", value="list"): assign character vectors in value to corresponding geneIds of object.
names: signature(x = "GeneSetCollection"): return the setName of each gene set in the colloection.

Logical and subsetting operations

union: 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.
intersect: 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.
setdiff: 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.

Additional useful methods.

updateObject: Objects created in previous versions of GSEABase may be incompatible with current object definitions. Usually this is singalled by an error suggesting that a slot is missing, and a recommnedation to use updateObject. Use updateObject to update a GeneSetCollection and all contained GeneSets to their current defintion.
mapIdentifiers: Convert genes from one GeneIdentifierType to another. See mapIdentifiers and specific methods in GeneIdentifierType for additional detail.
incidence: Summarize shared membership in genes across gene sets. See incidence-methods.
toGmt: Export to 'GMT' format file. See toGmt.
show: signature(object="GeneSetCollection"): provide a compact representation of object.

Martin Morgan <Martin.Morgan@RoswellPark.org>

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")])