snv.id.conversion: Mutation Matrix ID Conversion

In mehrankr/AbHAC: Aberration Hub Analysis of Cancer

Description

Converts non-uniprot rownames of mutation matrix to uniprot. merges rows that output rowname is same. IDs should be in one of these formats: entrez gene IDs, HGNC or ENSEMBL gene IDs

Usage

snv.id.conversion(snv = NULL, id.con.set = id.conversion.set)

Arguments

snv	for this function is a matrix of mutations with rownames as genes and colnames as samples
id.con.set	A dataframe for ID conversions provided as global variable id.conversion.set. Columns represent Entrez gene ID, Uniprot Accession, Gene Symbol, Ensembl gene ID and refseq protein ID (all human)

Value

This function finds uniprot IDs, removes rows without uniprot ID or duplicate uniprot ID

Author(s)

Mehran Karimzadeh mehran.karimzadehreghbati at mail dot mcgill dot ca

mehrankr/AbHAC documentation built on May 22, 2019, 6:49 p.m.