h_get_annotation_biomart: Get Annotations from 'BioMart'

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Get Annotations from BioMart

Description

Helper function to query annotations from biomaRt, for cleaned up gene IDs of a specific ID variable and given biomaRt::Mart.

Usage

h_get_annotation_biomart(gene_ids, id_var, mart)

Arguments

gene_ids	(character) gene IDs, e.g. 10329, i.e. already without the Entrez GeneID prefix, or ENSG00000241644 for Ensembl gene ID.
id_var	(string) corresponding gene ID variable name in BioMart, i.e. entrezgene_id or ensembl_gene_id.
mart	(Mart) given biomaRt::Mart object.

Value

A data frame with columns:

• id_var (depending on what was used)

• hgnc_symbol

• entrezgene_description

• chromosome_name

• size

• refseq_mrna

• refseq_peptide

Examples

if (interactive()) {
  mart <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  h_get_annotation_biomart(c("11185", "10677"), id_var = "entrezgene_id", mart = mart)
}

insightsengineering/hermes documentation built on Sept. 19, 2024, 9:06 p.m.