uniqGenesetsByNamespace: Make names of gene-sets unique by namespace, and member genes...

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

Description

Make names of gene-sets unique by namespace, and member genes of gene-sets unique

Usage

uniqGenesetsByNamespace(gmtList)

Arguments

gmtList

A GmtList object, probably from readGmt. The object must have namespaces defined by setNamespace. The function make sure that names of gene-sets within each namespace are unique, by merging gene-sets with duplicated names genes within each gene-set are unique, by removing duplicated genes Gene-sets with duplicated names and different desc are merged, desc are made unique, and in case of multiple values, concatenated (with | as the collapse character).

Value

A GmtList object, with unique gene-sets and unique gene lists. If not already present, a new item namespace is appended to each list element in the GmtList object, recording the namespace used to make gene-sets unique. The order of the returned GmtList object is given by the unique gene-set name of the input object.

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])))
 
print(myGmtList)
myGmtList <- setNamespace(myGmtList, namespace=function(x) x$desc)
myUniqGmtList <- uniqGenesetsByNamespace(myGmtList)
print(myUniqGmtList)

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