convert_symbols {aliases2entrez}

Multi resources gene symbols conversion to entrez ID (Human)

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returns a vector containing IDs if match were found or NA if unknown or withdrawn symbol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