mut.lik.change: Calculate change in likelihood due to background mutations

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

Description

This function calculates the change in likelihood for each existing mutation in the reformatted tables obtained from mut.type.converter given estimates of the relative rate parameters from fit.background.model.

Usage

  mut.lik.change(nonsil.mut.type, res, nonsilent, both_log,
    p_inframe, p_frameshift, p, r, s, epsilon, delta, gene)

Arguments

nonsil.mut.type	a reformatted mutation table that contains an extra two columns: 1. a mutation type indicator (1= transition, 2=transversion, and 3=indel), 2. SIFT score for the mutation. Second item returned from mut.type.converter.
res	a gene list obtained from generate.sel.exome and run through multiplyr for genes used for nonsilent rate estimation
nonsilent	logical value indicating whether genes are used for nonsilent rate estimation
both_log	logical value indicating whether genes are used for both silent and nonsilent rate estimation
p_inframe	numerical value representing the rate if in-frame indel mutations to A/T transitions
p_frameshift	numerical value representing the rate if frameshift indel mutations to A/T transitions
p	a vector of length 7 containing the mutation type relative rate parameters in the following order: A/T transition, A/T transversion, non-CpG transition, non-CpG transversion, CpG transition, CpG transversion, and Indel.
s	a vector of length 3 containing the relative rate parameters for the three replication timing regions (1=Early, 2=Middle, 3=Late)
epsilon	a vector of length 3 containing the relative rate parameters for the three expression levels (1=Low, 2=Medium, 3=High)
delta	vector of length 2 where the second element represents the relative rate of mutation in olfactory receptor (OR) genes compared to all others within a similar replication timing and expression level category. First element set to 1 (reference category).
gene	a list with one entry for each gene, each entry is another list of 5 elements: Ensembl name, chromosome, base pairs, replication timing region (1=Early, 2=Middle, 3=Late), and expression level (1=Low, 2=Medium, 3=High).
r	numeric value representing the relative rate parameter estimate for the ratio of mutations in genes with nonsilent vs only silent mutations (selection bias)

Value

a matrix containing the likelihood due to existing background mutations, to be utilized in calculate.bij

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.