TransGeneID: Gene ID conversion between ENTREZID and SYMBOL

In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

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")

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.