ensembl_to_hgnc: Get the hgnc gene symbol for an ensembl gene id.

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

Description

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

Usage

ensembl_to_hgnc(this_ensembl, all_genes_tbl)

Arguments

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

Details

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

Value

The matching hgnc gene symbol.

Author(s)

Ariane L. Moore

Examples

## Not run: 
all_genes_tbl <- create_ensembl_gene_tbl_hg()
ensembl_to_hgnc("ENSG00000134086", all_genes_tbl)
ensembl_to_hgnc("ENSG00000141510", 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] "VHL"
[1] "TP53"

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