multiply.p.s.epsilon: Multiply the constants in 'exome.constants' by the relative...

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

Description

A function to multiply the constants e, f, c, and d in exome.constants by the relative rate parameters of the background mutation model. The parameters used depend on the mutation type, nucleotide context of the position, and the replication timing region and expression level of the gene that the position resides in.

Usage

  multiply.p.s.epsilon(X, p, s, epsilon, delta, gene)

Arguments

X	a list with one entry for each chromosome, where each entry is a matrix containing a row for each coding base pair and the following columns: 1. base pair position, 2. nucleotide number (see convert.seq.to.num), 3. number of possible nonsilent transitions, 4. number of possible nonsilent transversions, 5. number of possible silent transitions, 6. number of possible silent transversions, and 7. whether the position is in a CpG dinucleotide.
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).

Value

an object of the same structure as exome.constants, but columns 3-6 (e, f, c, d) have been multiplied by relative rate parameters p, s, and epsilon.

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.