| Title: | Converts Human gene symbols to entrez IDs |
| Version: | 0.1.2 |
| 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). |
| BugReports: | https://github.com/peyronlab/aliases2entrez/issues |
| Imports: | doParallel, limma, utils, org.Hs.eg.db, AnnotationDbi, parallel, foreach, readr, RCurl |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.1.1 |
| Suggests: | spelling |
| Language: | en-US |
| NeedsCompilation: | no |
| Packaged: | 2021-02-15 09:48:25 UTC; raphael |
| Author: | Raphael Bonnet [aut, cre] (Université Côte d’Azur), Lee Mariault [ctb] (Université Côte d’Azur), Jean-François Peyron [aut] (Inserm) |
| Maintainer: | Raphael Bonnet <raphael.bonnet@univ-cotedazur.fr> |
| Repository: | CRAN |
| Date/Publication: | 2021-02-15 10:30:06 UTC |
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returns a vector containing IDs if match were found or NA if unknown or withdrawn symbol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)
Update last HGNC correspondence database
Description
This function is used to update gene symbol correspondence from HGNC database
Usage
update_symbols(url=NULL)
Arguments
url |
user can provide url (default is NULL) |
Value
returns a data.frame containing gene symbols with status, previous symbols and synonyms as well as their corresponding entrezIDs
Examples
HGNC <- update_symbols()