lupost.vec: Likelihood of mutations in a single gene and sample given the...

In kdkorthauer/MADGiC: Fits an empirical Bayesian hierarchical model to obtain posterior probabilities that each gene is a driver.

Description

Calculates, for a given gene and sample, the likelihood of mutations in a given gene under the background mutation model and current value of the sample-specific mutation rate

Usage

  lupost.vec(t, mutationexist, C, D, uniqueB, tableB,
    uniqueA, tableA, base)

Arguments

t	numeric value of sample-specific mutation rate (log-scale)
mutationexist	logical value indicating whether to include observed mutations in the current gene
C	subset of matrix muttable (see calculate.bij) containing only those rows corresponding to the current sample
D	numeric value corresponding to the sum of the logarithms of the first column of C
uniqueB	similar to uniqueA except restricted to the current gene
tableB	similar to tableA except restricted to the current gene
base	minimum value of the log likelihood of the sample-specific mutation rate q_j given the background model
uniqueA	a numeric vector containing all unique values of A (see getA)
tableA	a numeric vector of the same length of uniqueA that contains the number of instances of each value in uniqueA

Value

likelihood of mutations in a single gene and sample given the background model and sample-specific mutation rate t

Note

This internal function is not intended to be called by the user.

kdkorthauer/MADGiC documentation built on June 13, 2020, 1:35 p.m.