alias2Symbol {limma} | R Documentation |
Maps gene alias names to official gene symbols.
alias2Symbol(alias, species = "Hs", expand.symbols = FALSE) alias2SymbolTable(alias, species = "Hs")
alias |
character vector of gene aliases |
species |
character string specifying the species.
Possible values include |
expand.symbols |
logical.
This affects those elements of |
Aliases are mapped via NCBI Entrez Gene identity numbers using Bioconductor organism packages.
alias2Symbol
maps a set of aliases to a set of symbols, without necessarily preserving order.
The output vector may be longer or shorter than the original vector, because some aliases might not be found and some aliases may map to more than one symbol.
alias2SymbolTable
maps each alias to a gene symbol and returns a table with one row for each alias.
If an alias maps to more than one symbol, then the first one found is returned.
species
can be any character string XX for which an organism package org.XX.eg.db exists and is installed.
The only requirement of the organism package is that it contains objects org.XX.egALIAS2EG
and org.XX.egSYMBOL
linking the aliases and symbols to Entrez Gene Ids.
At the time of writing (June 2016), the following organism packages are available from Bioconductor:
Package | Species | |
org.Ag.eg.db | Anopheles | |
org.Bt.eg.db | Bovine | |
org.Ce.eg.db | Worm | |
org.Cf.eg.db | Canine | |
org.Dm.eg.db | Fly | |
org.Dr.eg.db | Zebrafish | |
org.EcK12.eg.db | E coli strain K12 | |
org.EcSakai.eg.db | E coli strain Sakai | |
org.Gg.eg.db | Chicken | |
org.Hs.eg.db | Human | |
org.Mm.eg.db | Mouse | |
org.Mmu.eg.db | Rhesus | |
org.Pt.eg.db | Chimp | |
org.Rn.eg.db | Rat | |
org.Ss.eg.db | Pig | |
org.Xl.eg.db | Xenopus |
Character vector of gene symbols.
alias2SymbolTable
returns a vector of the same length and order as alias
, including NA
values where no gene symbol was found.
alias2Symbol
returns an unordered vector that may be longer or shorter than alias
.
Gordon Smyth and Yifang Hu
This function is often used to assist gene set testing, see 10.GeneSetTests.
alias2Symbol(c("PUMA","NOXA","BIM"), species="Hs") alias2Symbol("RS1", expand=TRUE)