hgnc_to_ensembl: Get the ensembl gene id for a hgnc gene symbol.

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

Map a given hgnc gene symbol to the ensembl gene id.

Usage

hgnc_to_ensembl(this_hgnc, all_genes_tbl)

Arguments

this_hgnc	The hgnc gene symbol of a gene.
all_genes_tbl	A tibble with all genes ensembl id's and hgnc gene symbols.

Details

For a hgnc gene symbol and a tibble with all genes as input, this function returns the matching ensembl gene id. The tibble with all genes can be generated with create_ensembl_gene_tbl_hg.

Value

The matching ensembl gene id. In case several ensembl gene id's were found, they are all returned with ";" as a separator.

Author(s)

Ariane L. Moore

Examples

## Not run: 
all_genes_tbl <- create_ensembl_gene_tbl_hg()
hgnc_to_ensembl("VHL", all_genes_tbl)
hgnc_to_ensembl("PBRM1", all_genes_tbl)

## End(Not run)

Example output

GRCh version: 37, 
        and Ensembl Genes version: 88
Obtain a tibble with various gene id's and their genomic coordinates...
BiomaRt function call did not work. Possibly biomart or ensembl are currently down.
Here's the original error message:
Could not resolve host: www.ensembl.org
Load 'all_genes_tbl' from the GeneAccord saved data:
...done
[1] "ENSG00000134086"
[1] "ENSG00000163939"

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.