Description Usage Arguments Value Author(s) Examples
Gene ID conversion between ENTREZID and SYMBOL
1 2 3 4 5 6 7 8 9 10 11 | TransGeneID(
genes,
fromType = "Symbol",
toType = "Entrez",
organism = "hsa",
fromOrg = organism,
toOrg = organism,
ensemblHost = "www.ensembl.org",
unique = TRUE,
update = FALSE
)
|
genes |
A character vector, input genes to be converted. |
fromType |
The input ID type, one of "entrez", "symbol"(default), "hgnc", "ensembl", "fullname" and "uniprotswissprot"; you can also input other valid attribute names for biomaRt. Look at the code in examples to check valid attributes. |
toType |
The output ID type, similar to 'fromType'. |
organism |
"hsa"(default), "mmu", "bta", "cfa", "ptr", "rno", and "ssc" are optional. |
fromOrg |
"hsa", "mmu", "bta", "cfa", "ptr", "rno", and "ssc" are optional (Only used when transform gene ids between organisms). |
toOrg |
"hsa"(default), "mmu", "bta", "cfa", "ptr", "rno", and "ssc" are optional (Only used when transform gene ids between organisms). |
ensemblHost |
String, specifying ensembl host, you can use 'listEnsemblArchives()' to show all available Ensembl archives hosts. |
unique |
Boolean, specifying whether do one-to-one mapping. |
update |
Boolean, specifying whether update built-in gene annotation (needs network and takes time). |
A character vector, named by unique input gene ids.
Wubing Zhang
1 2 3 | TransGeneID("HLA-A", organism="hsa")
TransGeneID("HLA-A", toType = "uniprot", organism="hsa")
TransGeneID("H2-K1", toType="Symbol", fromOrg = "mmu", toOrg = "hsa")
|
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