convert_ensembl_to_reactome_pw_tbl {GeneAccord}R Documentation

Map ensembl gene id clone tibble to reactome pathway clone tibble.

Description

For a tibble that contains the information which ensembl gene id is mutated in which clone, map the ensembl gene id to the reactome pathways that contain this gene.

Usage

convert_ensembl_to_reactome_pw_tbl(mutated_gene_tbl, ensg_reactome_path_map)

Arguments

mutated_gene_tbl

The tibble containing the information of which ensembl gene id is altered in which patient and clone. Can be created with e.g. create_tbl_ent_clones.

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

Such a tibble can be generated with e.g. the function create_tbl_tree_collection. If the altered entities in the lists were the ensembl gene id's, this function can convert the tibble into a tibble with the altered reactome pathways. It has the columns 'file_name', 'patient_id', 'altered_entity', 'clone1', 'clone2', ... up to the maximal number of clones (Default: until 'clone7'). If the mutated entities are ensembl gene id's, they can be mapped with this function to the pathways from 'reactome'. The pathways are from the lowest level of hierarchy.

Value

The tibble containing the information of which pathway is altered in which clone.

Author(s)

Ariane L. Moore

Examples

data("ensg_reactome_path_map")
mutated_gene_tbl <- 
  dplyr::tibble(file_name=c("pat1.csv", "pat1.csv"),
patient_id=c("1","1"),
altered_entity=c("ENSG00000134086", 
"ENSG00000141510"),
clone1=c(1,0),
clone2=c(0,1))
convert_ensembl_to_reactome_pw_tbl(mutated_gene_tbl, 
    ensg_reactome_path_map)

[Package GeneAccord version 1.11.0 Index]