setNamespace.Rd
Set the namespace field in each gene-set within a GmtList
setNamespace(x, namespace)
x | A |
---|---|
namespace | It can be either a function that applies to a Note that using vectors as |
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#> [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"#> [1] FALSE