SLAPE.check_and_fix_gs_Dataset: Check and fix gene symbol names in a genomic event dataset

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

Description

This function checks that the row names of a genomic dataset are actually updated official gene symbols approved by the HUGO Gene Nomenclature Committee (HGNC) (http://www.genenames.org).

Usage

SLAPE.check_and_fix_gs_Dataset(Dataset, updated.hgnc.table)

Arguments

Dataset	An integer matrix modeling a genomic event dataset where row names are gene symbols and column names are sample identifiers. A non-null entry in the i,j position indicates the presence of a somatic mutation hosted by the i-th gene in the j-th sample (if the matrix is binary) or the number of point mutations hosted by the i-th gene in the j-th sample (if the matrix contains integers).
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

The integer matrix provided in input but with row names updated to the most recent approved gene symbol and rows with not found gene synonyms as names removed.

Author(s)

Francesco Iorio - [e-mail]

See Also

SLAPE.update_HGNC_Table, SLAPE.hgnc.table

Examples

data(LUAD_CaseStudy)
data(SLAPE.hgnc.table)
updatedGeneSymbolsDataset<-SLAPE.check_and_fix_gs_Dataset(LUAD_CaseStudy,hgnc.table)

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