get_hist_clon_excl: Compute all values of how often gene pairs were clonally...

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

Description

Compute all values of how often gene pairs were clonally exclusive/all trees for a patient.

Usage

get_hist_clon_excl(clone_tbl)

Arguments

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.

Details

It computes a histogram of the following two values: Amomg all gene/pathway pairs in a patient, the number of trees in which the both entities of a pair are assigned to a clone at all, and the number of trees in which the pair is clonally exclusive.

Value

A list with two vectors: The numbers of how often gene pairs were mutated across trees, and the numbers of how often they were clonally exclusive. The order of these two vectors is matching, i.e. the ith entry in each vector refers to the same gene pair.

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(clone_tbl)

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