get_genes_by_GO: Get genes related to certain GO terms from biomart database

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

Get genes related to certain GO terms from biomart database

Description

Get genes related to certain GO terms from biomart database

Usage

get_genes_by_GO(
  returns = "ensembl_gene_id",
  dataset = "mmusculus_gene_ensembl",
  go = NULL
)

Arguments

returns	the gene id which is set as return. Default to be ensembl id A possible list of attributes can be retrieved using the function listAttributes from biomaRt package. The commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene'.
dataset	Dataset you want to use. List of possible datasets can be retrieved using the function listDatasets from biomaRt package.
go	a vector of GO terms

Details

Get genes related to certain GO terms from biomart database

Value

a vector of gene ids.

Examples

# get all genes under GO term GO:0005739 in mouse, return ensembl gene id
get_genes_by_GO(returns="ensembl_gene_id",
    dataset="mmusculus_gene_ensembl",
    go=c('GO:0005739'))

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.