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

In Accio/BioQC: Detect tissue heterogeneity in expression profiles with gene sets

Description

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

Usage

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.

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)
myGmtList2 <- setNamespace(myGmtList, namespace=function(x) x$desc)
gsNamespace(myGmtList2)
## the function can provide flexible ways to encode the gene-set namespace
myGmtList3 <- setNamespace(myGmtList, namespace=function(x) gsub("Namespace", "C", x$desc))
gsNamespace(myGmtList3)
## using vectors
myGmtList4 <- setNamespace(myGmtList, namespace=c("C1", "C1", "C1", "C2"))
gsNamespace(myGmtList4)
myGmtList2null <- setNamespace(myGmtList2, namespace=NULL)
hasNamespace(myGmtList2null)

Accio/BioQC documentation built on Jan. 27, 2022, 10:45 p.m.