list_omim_accessions: List the available OMIM morbid IDs and descriptions

In MCorentin/vargen: Fetching Variants Related to Phenotypes Using Public Databases

List the available OMIM morbid IDs and descriptions

Description

List the "OMIM IDs" available in biomaRt, will also print the corresponding description. Use getBM with the following filter: "with_mim_morbid". This function is useful to get OMIM IDs for get_omim_genes

Usage

list_omim_accessions(gene_mart, keywords)

Arguments

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).
keywords	a vector containing a list of keywords. This will be grepped (case insensitive) against the list of omim descriptions to retrieve a list of omim IDs.

Value

a dataframe with two columns ("mim_morbid_accession" and "mim_morbid_description")

Examples

gene_mart <- connect_to_gene_ensembl()
list_omim_accessions(gene_mart)
list_omim_accessions(gene_mart, "alzheimer")
list_omim_accessions(gene_mart, c("alzheimer", "obesity"))

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