alias2Symbol {limma} | R Documentation

## Convert Gene Aliases to Official Gene Symbols

### Description

Maps gene alias names to official gene symbols.

### Usage

    alias2Symbol(alias, species = "Hs", expand.symbols = FALSE)
    alias2SymbolTable(alias, species = "Hs")
    alias2SymbolUsingNCBI(alias, gene.info.file,
                          required.columns = c("GeneID","Symbol","description"))

### Arguments

`alias` | character vector of gene aliases
`species` | character string specifying the species. Possible values include `"Hs"` (human), `"Mm"` (mouse), `"Rn"` (rat), `"Dm"` (fly) or `"Pt"` (chimpanzee), but other values are possible if the corresponding organism package is available.
`expand.symbols` | logical. This affects those elements of `alias` that are the official gene symbol for one gene and also an alias for another gene. If `FALSE`, then these elements will just return themselves. If `TRUE`, then all the genes for which they are aliases will also be returned.
`gene.info.file` | either the name of a gene information file downloaded from the NCBI or a data.frame resulting from reading such a file.
`required.columns` | character vector of columns from the gene information file that are required in the output.

### Details

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` returns of vector of the same length as the vector of aliases. If an alias maps to more than one symbol, then the one with the lowest Entrez ID number is returned. If an alias can't be mapped, then `NA` 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, the following organism packages are available from Bioconductor 3.6:

| 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

`alias2SymbolUsingNCBI` is analogous to `alias2SymbolTable` but uses a gene-info file from NCBI instead of a Bioconductor organism package. It also gives the option of returning multiple columns from the gene-info file. NCBI gene-info files can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO. For example, the human file is ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz and the mouse file is ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz.

### Value

`alias2Symbol` and `alias2SymbolTable` produce a 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`.

`alias2SymbolUsingNCBI` returns a data.frame with rows corresponding to the entries of `alias` and columns as specified by `required.columns`.

### Author(s)

Gordon Smyth and Yifang Hu

### See Also

This function is often used to assist gene set testing, see 10.GeneSetTests.

### Examples

    alias2Symbol(c("PUMA","NOXA","BIM"), species="Hs")
    alias2Symbol("RS1", expand=TRUE)

[Package limma version 3.42.2 Index]