merge_clones_identical_ents: Merge identical entities in clone tibble from one patient

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

Description

Merge clone profile of identical entities in clone tibble from one patient

Usage

merge_clones_identical_ents(clone_tbl)

Arguments

clone_tbl

The clone tibble as generated with create_tbl_ent_clones from one patient.

Details

Given a clone tibble as created with create_tbl_ent_clones from one patient and where the entities were possibly mapped from genes to pathways, this function checks whether there were several entities mapped to the same new entity. If so, the clone profile will be merged. This can be the case, for instance, of two mutated genes are in the same pathway(s).

Value

The same tibble but in case there were several identical genes/pathways in the same patient with different clone profiles, their profile will be merged together. This can happen if, e.g. two genes with different clone profiles are in the same pathway. When mapping them to the pathways, there will be two identical 'altered_entities' with different clone profiles. These profiles would be merged by this function because the pathway is affected in the union of clones were the two genes were mutated.

Author(s)

Ariane L. Moore

Examples

clone_tbl <- dplyr::tibble(
    file_name=c(rep("fn1", 4)),
    patient_id=c(rep("pat1", 4)),
    altered_entity=c("pw1", "pw1", 
                       "pw2", "pw3"),
    clone1=c(1, 0, 1, 0),
    clone2=c(0, 1, 0, 1),
    clone3=c(1, 1, 0, 1),
    clone4=c(0, 1, 0, 0))
merge_clones_identical_ents(clone_tbl)

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