Set the namespace field in each gene-set within a GmtList

setNamespace(x, namespace)

Arguments

x	A `GmtList` object encoding a list of gene-sets
namespace	It can be either a function that applies to a `gene-set list` element of the object (for instance `function(x) x$desc` to extract description), or a vector of the same length of `x`, or in the special case `NULL`, which will erase the field namespace. Note that using vectors as `namespace` leads to poor performance when the input object has many gene-sets.

A GmtList object encoding a list of gene-sets

namespace

It can be either a function that applies to a gene-set list element of the object (for instance function(x) x$desc to extract description), or a vector of the same length of x, or in the special case NULL, which will erase the field namespace.

Note that using vectors as namespace leads to poor performance when the input object has many gene-sets.

Examples

myGmtList <- GmtList(list(list(name="GeneSet1", desc="Namespace1", genes=LETTERS[1:3]),
  list(name="GeneSet2", desc="Namespace1", genes=rep(LETTERS[4:6],2)),
  list(name="GeneSet1", desc="Namespace1", genes=LETTERS[4:6]),
  list(name="GeneSet3", desc="Namespace2", genes=LETTERS[1:5])))
hasNamespace(myGmtList)
#> [1] FALSE
myGmtList2 <- setNamespace(myGmtList, namespace=function(x) x$desc)
gsNamespace(myGmtList2)
#> [1] "Namespace1" "Namespace1" "Namespace1" "Namespace2"
## the function can provide flexible ways to encode the gene-set namespace
myGmtList3 <- setNamespace(myGmtList, namespace=function(x) gsub("Namespace", "C", x$desc))
gsNamespace(myGmtList3)
#> [1] "C1" "C1" "C1" "C2"
## using vectors
myGmtList4 <- setNamespace(myGmtList, namespace=c("C1", "C1", "C1", "C2"))
gsNamespace(myGmtList4)
#> [1] "C1" "C1" "C1" "C2"
myGmtList2null <- setNamespace(myGmtList2, namespace=NULL)
hasNamespace(myGmtList2null)
#> [1] FALSE