get_rate_diff_branch_ent_pair: Compute rate of being in different branches/clones.

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

Description

Compute the rate of mutated gene/pathway pairs being in different branches.

Usage

get_rate_diff_branch_ent_pair(clone_tbl)

Arguments

clone_tbl

A tibble containing the columns 'altered_entity', and then a column for each clone

Details

Given the output of a tool that identifies clones within tumors and their phylogenetic history, this function computes the rate of mutated gene/pathway pairs being in different branches. That is, it will calculate the number of times mutated gene/pathway pairs are in different branches/clones divided by the total number of all mutated gene/pathway pairs.

Value

The rate of occurrence of mutated gene/pathway pairs being in different clones.

Author(s)

Ariane L. Moore in the tumor, e.g. 'clone1', 'clone2', 'clone3'. This tibble can be generated e.g. from the Cloe output.

Examples

clone_tbl <- dplyr::tibble(
    altered_entity=c(paste("gene", seq_len(10), sep="")),
    clone1=c(rep(0,10)),
    clone2=c(sample(c(0,1), 10, replace=TRUE)),
    clone3=c(sample(c(0,1), 10, replace=TRUE)),
    clone4=c(sample(c(0,1), 10, replace=TRUE)))
get_rate_diff_branch_ent_pair(clone_tbl)

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