get_hist_clon_excl_this_pat_this_pair: Check for a pair how often it was mutated in the current...

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

Description

Check for a pair how often it was mutated in the current patient across trees, and how often also clonally exclusive.

Usage

get_hist_clon_excl_this_pat_this_pair(entA, entB, clone_tbl)

Arguments

entA	One gene/pathway of the pair
entB	The other gene/pathway of 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'. It also contains the column 'tree_id', which specifies which tree of the collection of tree inferences was used. This tibble can be generated e.g. from the Cloe output.

Value

A vector with the values of in how many trees the pair was mutated, and in how many of those it was clonally exclusive.

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)),
    tree_id=c(rep(5, 5), rep(10, 5)) )
get_hist_clon_excl_this_pat_this_pair("gene1", "gene2", clone_tbl)

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