setNamespace {BioQC} | R Documentation

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

### 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)

[Package BioQC version 1.18.0 Index]