SLAPE.check_and_fix_path_collection: Check and fix gene symbol names in a collection of pathway...

In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description

This function checks that gene identifiers contained in a pathway gene set collection are actually updated official gene symbols approved by the HUGO Gene Nomenclature Committee (HGNC) (http://www.genenames.org).

Usage

SLAPE.check_and_fix_path_collection(pathColl, updated.hgnc.table)

Arguments

pathColl	A list containing pathway gene-sets and annotations.
updated.hgnc.table	A data frame containing up-to-date approved HGNC symbols (Approved.Symbol variable) and their synonyms (Symbol variable). This is availalbe in the SLAPE.hgnc.table data object or can be created by downloading updated relevant information from the HUGO Gene Nomenclature Committee web-portal (http://www.genenames.org), using the function SLAPE.update_HGNC_Table.

Value

Pathway collection provided in input but with gene identifiers updated to the most recent approved gene symbols and not approved symbols removed.

Author(s)

Francesco Iorio - [e-mail]

See Also

SLAPE.update_HGNC_Table, SLAPE.hgnc.table

Examples

data(SLAPE.PATHCOM_HUMAN)
data(SLAPE.hgnc.table)
updatedGeneSymbolsDataset<-
SLAPE.check_and_fix_path_collection(PATHCOM_HUMAN,hgnc.table)

saezlab/SLAPenrich documentation built on May 29, 2019, 12:57 p.m.