get_omim_genes: Get ensembl gene IDs from "mim_morbid_accession"

View source: R/omim.R

get_omim_genesR Documentation

Get ensembl gene IDs from "mim_morbid_accession"

Description

Use getBM to filter results by "mim_morbid_accession". One or more accessions can be given as input.

Usage

get_omim_genes(omim_ids, gene_mart)

Arguments

omim_ids

is a vector of morbity accession eg: c("125853","222100") for Diabetes

gene_mart

a connection to hsapiens gene mart, can be generated from connect_to_gene_ensembl (which will be used if this argument if not specified).

Value

a dataframe with

  • ensembl_gene_id (ensembl stable gene ID, eg:"ENSG00000134640")

  • chromosome_name (chromosome name)

  • start_position (gene start)

  • end_position (gene end)

  • hgnc_symbol (gene id from the Hugo Gene Nomenclature Committee, eg:"MTNR1B")

  • mim_morbid_accession (the OMIM morbid ID, eg:"125853")

  • mim_morbid_accession (the OMIM description, eg: "NONINSULIN-DEPENDENT DIABETES MELLITUS")

Examples

gene_mart <- connect_to_gene_ensembl()
DM_genes <- get_omim_genes(c("125853","222100"), gene_mart)

MCorentin/vargen documentation built on Feb. 6, 2024, 2:32 p.m.