ensembl_to_reactome: Get the reactome pathways 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 reactome pathways that contain this gene.

Usage

ensembl_to_reactome(this_ensembl, ensg_reactome_path_map)

Arguments

this_ensembl	The ensembl id of a gene.
ensg_reactome_path_map	A tibble with all ensembl id's and their reactome pathways. Can be loaded with data("ensg_reactome_path_map").

Details

As input, an ensembl gene id is given as well as the tibble 'ensg_reactome_path_map'. It can be loaded with data("ensg_reactome_path_map"), and contains the ensembl gene id to reactome pathway mappings. The reactome pathways are from the lowest level of the hierarchy. This function returns the reactome pathways for the input gene.

Value

The pathways that contain this gene as a character vector.

Author(s)

Ariane L. Moore

Examples

data("ensg_reactome_path_map")
ensg_gene <- "ENSG00000134086"
ensembl_to_reactome(ensg_gene, ensg_reactome_path_map)

Example output

The ensembl ID ENSG00000134086 was mapped to 3 reactome pathways.
[1] "Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha"
[2] "Neddylation"                                                             
[3] "Antigen processing: Ubiquitination & Proteasome degradation"             

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