create_ensembl_gene_tbl_hg: Get a tibble of all gene ensembl id's, gene names (hgnc),...

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

Description

Retrieve a mapping between different gene identifiers.

Usage

create_ensembl_gene_tbl_hg(GRCh = 37, ensembl_version = 88)

Arguments

GRCh	The human genome version. Default: 37.
ensembl_version	The version of the ensembl data base. Default: 88.

Details

This function retrieves the ensembl gene id's from biomart together with the hgnc gene symbol, the entrez gene id, the uniprot/swissprot gene id, as well as chromosome, start and end position. This is done for the human genes from the human genome version hg19/GRCh37, and Ensembl Genes version 88. The user can also specify other human genome or ensembl versions.

Value

A tibble with the following columns: ensembl_gene_id, hgnc_symbol, entrezgene, uniprotswissprot, chromosome_name, start_position, end_position. The entrez gene id, as well as the start and end positions are numeric, and the other columns are characters. The chromosome is specified without "chr", i.e. the chromosome 13 for example, would be specified with "13".

Author(s)

Ariane L. Moore

Examples

## Not run: 
create_ensembl_gene_tbl_hg()

## End(Not run)

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