Hugo
An R package to retrieve and convert genes names according to the Hugo Gene Nomenclature Committee (HGNC)

Licence: GPL
Dev. status: beta
Bugs report: alain.viari@inria.fr
(don't expect strong responsiveness)


Note: If you are a 'data.table' guru then you better have to download the tab file from HGNC, and process it manually with 'data.table'.
However it usually takes me some hours to remember all the arcana of 'data.table'.
This is the reason why I wrapped them into few functions provided in this package.
Also, since a long time, I wanted to write an R package named as 'hugo', so I jumped on this opportunity.
Installation
1. Download the latest version from Inria GForge

2. Install in R as:
install.packages("hugo_<version>.tar.gz", repos=NULL, type="source")

3. (mandatory) If not already done, install the 'data.table' package from CRAN
install.packages("data.table")
Sample
library(hugo) # load db db <- hugo.load() # converting names sym <- c("TP53", "ERDA1", "U3", "TPT", "not.here", "tp53") ens <- hugo.convert(db, sym, to="ensembl", aliases=TRUE, ignore.case=TRUE) ens <- hugo.convert(db, sym, to="ensembl", aliases=TRUE, ignore.case=TRUE, multiple="first") hugo.convert(db, na.omit(ens), from="ensembl", to="cosmic") # fetching information hugo.fetch(db, from="symbol") hugo.fetch(db, from="symbol", to="ensembl", na.values="remove") hugo.fetch(db, from="symbol", to=c("ensembl", "enzyme"), na.values="remove") hugo.fetch(db, from="ensembl", to=c("symbol", "alias_symbol", "cosmic")) table(hugo.fetch(db, to="locus_group")$locus_group) hugo.fetch(db, query=c("tP53", "U3", "TpT"), to=c("ensembl", "hgnc"), aliases=TRUE, ignore.case=TRUE, multiple="collapse") hugo.fetch(db, query="17q12", from="location", to=c("symbol", "ensembl")) hugo.fetch(db, query=c("^A", "^b"), to="name", ignore.case=TRUE, regexp=TRUE)
Documentation
pdf