bio_geneid: Function to switch Gene Ids

In KatrionaGoldmann/BioOutputs: Visualisation of Biological Data

Function to switch Gene Ids

Description

This function switches gene (or snp) ids using biomart

Usage

bio_geneid(
  IDs,
  IDFrom = "ensembl_transcript_id",
  IDTo = "hgnc_symbol",
  mart = "ensembl",
  dataset = "hsapiens_gene_ensembl",
  attributes = c("chromosome_name", "start_position", "end_position")
)

Arguments

IDs	list of the Ids you want to convert
IDFrom	What format these IDs are in (default Ensembl)
IDTo	What format you want the IDs converted to (default gene names)
mart	The biomart to use. Typically, for humans you will want ensembl (default). Alternatives can be found at listEnsembl()
dataset	you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useEnsembl('ENSEMBL_MART_ENSEMBL'), followed by listDatasets(mart).
attributes	list of variables you want output

Examples

IDs = c("TNF", "A1BG", "FOX3")
bio_geneid(IDs, IDFrom='hgnc_symbol', IDTo = 'ensembl_transcript_id')

KatrionaGoldmann/BioOutputs documentation built on May 21, 2022, 1:24 p.m.