compute_test_stat_avg_rate: Compute the test statistic of the clonal exclusivity test...

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

Description

Compute test statistic that is based on the average rates of clonal exclusivity of a patient, and the observed number of times a pair was clonally exclusive across several trees of the tree inference.

Usage

compute_test_stat_avg_rate(avg_rates_m, num_trees_pair, num_clon_excl)

Arguments

avg_rates_m	The vector of average rates of clonal exclusivity of each patient the pair is mutated in. It was computed for each patient separately, and is averaged over all gene pairs and all trees. Expected to be in the same (patient) order as the other inputs to this function.
num_trees_pair	The vector with the number of tree inferences in which the pair was occurring in. Has to be the same order as avg_rates_m.
num_clon_excl	The vector with the number of times the pair was clonally exclusive in the trees in each patient. Has to be the same order as avg_rates_m.

Details

For a given gene/pathway pair, this function takes as input: the average rates of clonal exclusivity of all patients in which the pair is mutated, the number of trees among the trees in the collection of trees from each patient in which the pair was occurring, and the number of times it was clonally exclusive

Value

A list with the test statistic of the clonal exclusivity test (lrtest), and the maximum likelihood estimate of delta.

Author(s)

Ariane L. Moore

Examples

compute_test_stat_avg_rate(c(0.1, 0.2), c(10, 10), c(9, 7))
compute_test_stat_avg_rate(c(0.05, 0.23), c(20, 20), c(8, 5))

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