results_tracker: Initialize the mutation event tracker tibble

In jhrcook/wext: Weighted Exclusivity Test (WExT)

Description

A tibble that contains the gene sets to consider mutual exclusivity or co-mutation between. This uses a bit of logic to reduce the number of gene sets to consider by accounting the for test at hand (exclusivity or co-mutation), the minimum mutations in a gene to consider it in any gene sets, and a seed gene is the user is interested in interactions with only one or a few genes.

Usage

make_empty_results_tracker(bgr, k, which_test, seed_genes, min_times_mut)

exclusivity_results_tracker(bgr, k, seed_genes, min_times_mut)

comutation_results_tracker(bgr, k, seed_genes, min_times_mut)

make_combs_tibble(genes, k, seed_genes)

Arguments

bgr	a bipartite edge graph that has the node attributes type and name; these attributes are not checked for explicitly, but will throw an error if not present
k	size of gene sets to consider (default is 2)
which_test	test for mutual exclusivity ("exclusivity") or co-mutation ("comutation"); (default is "comutation")
seed_genes	a vector of gene(s) that must be in the gene set to be tested (optional)
min_times_mut	minimum number of times a gene must be mutated in all samples to be considered for the gene sets (default is 5)
genes	a vector of gene(s) to make combinations of size k from

Value

A tibble with two columns: gene_sets contains list objects of k genes, t_BM_gr is a column of zeros that will eventually hold the number of events (either mutual exclusivity or co-mutation) that occur between the genes in the gene sets in the permuted bipartite graphs

Functions

• exclusivity_results_tracker: Create the tracker when testing for mutual exclusivity.

• comutation_results_tracker: Create the tracker when testing for co-mutation.

• make_combs_tibble: Create the final tibble object with the gene sets of size k.

Examples

library(wext)
bgr <- make_sample_gene_bipartite(
    simple_dataset$sample_name,
    simple_dataset$mutated_gene
)
make_empty_results_tracker(bgr, 2, "exclusivity", c(), 2)

jhrcook/wext documentation built on May 17, 2021, 1:19 a.m.