compute_rates_clon_excl: Get rates of clonal exclusivity for each tree inference

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

Description

Compute the clonal exclusivity rates for each gene-to-clone-assignment from the collection of tree inferences.

Usage

compute_rates_clon_excl(pat_tbl)

Arguments

pat_tbl

A tibble with the information of which gene/pathway is altered in which clone in the patient, and including this information from the collection of trees. Can be created with with create_tbl_tree_collection.

Details

Takes the gene-to-clone assignment tibble as created with create_tbl_tree_collection and computes for each instance from the collection of trees the rate of clonal exclusivity. This rate is the fraction of gene/pathway pairs that were on a different branch in the tumor phylogeny, i.e. the fraction of pairs that was clonally exclusive.

Value

A vector with all rates of clonal exclusivity from all tree inferences.

Author(s)

Ariane L. Moore

Examples

clone_tbl <- dplyr::tibble(file_name =
    rep("fn1", 10),
    "patient_id"=rep("pat1", 10),
    "altered_entity"=paste0("gene", 
    LETTERS[seq_len(10)]),
    "clone1"=c(0, 1, 0, 1, 0, 1, 0, 1, 1, 1),
    "clone2"=c(1, 0, 1, 0, 1, 1, 1, 0, 0, 1),
    "tree_id"=c(rep(1, 5), rep(2, 5)))
compute_rates_clon_excl(clone_tbl)

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