TransGeneID: Gene ID conversion between ENTREZID and SYMBOL

In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

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",
  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.
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("NFE2L2", organism="hsa")
TransGeneID("NFE2L2", toType="uniprot")

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.