Get Annotations from BioMart — h_get_annotation_biomart • hermes

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

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)
}