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

In scPipe: pipeline for single cell RNA-seq data analysis

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'))

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.