is_diff_branch_ent_pair: Check whether pair is in different branches/clones.

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

Description

Check whether a given pair of mutated genes/pathways is in different branches/clones.

Usage

is_diff_branch_ent_pair(ent1, ent2, clone_tbl)

Arguments

ent1	One mutated gene/pathway from the pair.
ent2	The other mutated gene/pathway from the pair.
clone_tbl	A tibble containing the columns 'altered_entity', and then a column for each clone in the tumor, e.g. 'clone1', 'clone2', 'clone3'. This tibble can be generated e.g. from the Cloe output.

Details

Given two mutated genes or pathways and the clone tibble as described in get_rate_diff_branch_ent_pair, this function returns TRUE or FALSE for whether the pair is mutated in different branches/clones.

Value

TRUE or FALSE for whether or not the pair is mutated in different clones/in different branches of the tree.

Author(s)

Ariane L. Moore

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)))
is_diff_branch_ent_pair("gene1", "gene2", clone_tbl)

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