setNamespace {BioQC} | R Documentation |
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) 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)