TransGeneID {MAGeCKFlute} | R Documentation

## Gene ID conversion between ENTREZID and SYMBOL

### Description

Gene ID conversion between ENTREZID and SYMBOL

### Usage

    TransGeneID(
      genes,
      fromType = "Symbol",
      toType = "Entrez",
      organism = "hsa",
      fromOrg = organism,
      toOrg = organism,
      ensemblHost = "www.ensembl.org",
      unique = TRUE,
      update = FALSE
    )

### Arguments

`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).

### Value

A character vector, named by unique input gene ids.

### Author(s)

Wubing Zhang

### Examples

    TransGeneID("HLA-A", organism="hsa")
    TransGeneID("HLA-A", toType = "uniprot", organism="hsa")
    TransGeneID("H2-K1", toType="Symbol", fromOrg = "mmu", toOrg = "hsa")

[Package MAGeCKFlute version 1.12.0 Index]