alias2Symbol(alias, species = "Hs", expand.symbols = FALSE)
alias2SymbolTable(alias, species = "Hs")"Hs" (human), "Mm" (mouse), "Rn" (rat), "Dm" (fly) or "Pt" (chimpanzee), but other values are possible if the corresponding organism package is available.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 be returned.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.
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 |
alias2Symbol(c("PUMA","NOXA","BIM"), species="Hs")
alias2Symbol("RS1", expand=TRUE)
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