map_pairs_to_hgnc_symbols: Map the ensembl gene ids to hgnc symbols from a tibble

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

Description

Map the ensembl gene ids to hgnc symbols from a tibble with pairs.

Usage

map_pairs_to_hgnc_symbols(pairs_of_interest_tbl, all_genes_tbl)

Arguments

pairs_of_interest_tbl	A tibble containing pairs of mutated genes/pathways. More precisely, it contains the columns 'entity_A' and 'entity_B'.
all_genes_tbl	A tibble with all genes ensembl id's and hgnc symbols. Can be created with create_ensembl_gene_tbl_hg.

Details

After having extracted the pairs of interest, it is of interest to know the genes hgnc symbols of the pairs. Here, it is assumed that the current gene identifier of the pairs are ensembl gene ids. They will be mapped to the corresponding hgnc symbols.

Value

A tibble similar to the input pairs_of_interest_tbl but with two additional columns, namely 'hgnc_gene_A', and 'hgnc_gene_B'. The column 'hgnc_gene_A' contains the hgnc gene symbol of 'entity_A', and the column 'hgnc_gene_B' the one of 'entity_B'.

Author(s)

Ariane L. Moore

Examples

## Not run: 
pairs_of_interest <- dplyr::tibble(
    entity_A=c("ENSG00000181143", "ENSG00000163939"),
    entity_B=c("ENSG00000141510", "ENSG00000163930"))
all_genes_tbl <- create_ensembl_gene_tbl_hg()
map_pairs_to_hgnc_symbols(pairs_of_interest, 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
# A tibble: 2 x 4
  entity_A        entity_B        hgnc_gene_A hgnc_gene_B
  <chr>           <chr>           <chr>       <chr>      
1 ENSG00000181143 ENSG00000141510 MUC16       TP53       
2 ENSG00000163939 ENSG00000163930 PBRM1       BAP1       

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