convert_symbols: Multi resources gene symbols conversion to entrez ID (Human)

In aliases2entrez: Converts Human gene symbols to entrez IDs

Description

This function is used to convert gene symbols, previous symbols or aliases to gene entrez ID
It performs :
-a gene query to limma::alias2Symbol to map gene alias to official symbols
-looks for LOC* symbols
-tries to find correspondence within HGNC database
-queries org.Hs.eg.db
-checks again with adaptive symbol parsing (e.g. transforms BRCA-1 to BRCA1)

Usage

convert_symbols(symbols,HGNC,c=1)

Arguments

symbols	gene matrix from which rownames (gene symbols) are extracted
HGNC	HGNC correspondence file.
c	number of cores to use for parallel processes

Value

returns a vector containing IDs if match were found or NA if unknown or withdrawn symbol

Examples

# import the correspondence file
file <- system.file("extdata", "HGNC.txt", package = "aliases2entrez")
HGNC <- read.delim(file)
# alternatively update a new one with update_symbols()
symbols <- c("BRCA1", "TP53")
# run the main function
ids <- convert_symbols(symbols, HGNC)

Example output

calling limma::alias2Symbol on provided data
-> matching 2 symbols to HGNC Approved symbol
all symbols found

aliases2entrez documentation built on Feb. 15, 2021, 5:07 p.m.