| Title: | Converts Human gene symbols to entrez IDs |
|---|---|
| Description: | Queries multiple resources authors HGNC (2019) <https://www.genenames.org>, authors limma (2015) <doi:10.1093/nar/gkv007> to find the correspondence between evolving nomenclature of human gene symbols, aliases, previous symbols or synonyms with stable, curated gene entrezID from NCBI database. This allows fast, accurate and up-to-date correspondence between human gene expression datasets from various date and platform (e.g: gene symbol: BRCA1 - ID: 672). |
| Authors: | Raphael Bonnet [aut, cre] (Université Côte d’Azur), Lee Mariault [ctb] (Université Côte d’Azur), Jean-François Peyron [aut] (Inserm) |
| Maintainer: | Raphael Bonnet <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.2 |
| Built: | 2024-10-12 05:57:16 UTC |
| Source: | https://github.com/peyronlab/aliases2entrez |
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)
convert_symbols(symbols,HGNC,c=1)convert_symbols(symbols,HGNC,c=1)
symbols |
gene matrix from which rownames (gene symbols) are extracted |
HGNC |
HGNC correspondence file. |
c |
number of cores to use for parallel processes |
returns a vector containing IDs if match were found or NA if unknown or withdrawn symbol
# 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)# 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)
This function is used to update gene symbol correspondence from HGNC database
update_symbols(url=NULL)update_symbols(url=NULL)
url |
user can provide url (default is NULL) |
returns a data.frame containing gene symbols with status, previous symbols and synonyms as well as their corresponding entrezIDs
HGNC <- update_symbols()HGNC <- update_symbols()