multiplyr: Multiply the nonsilent constants in a subsetted...

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 and f in a subsetted exome.constants object by the relative rate parameter for selection bias of the background mutation model. This parameter represents the ratio of nonsilent to silent mutations

Usage

  multiplyr(res, r)

Arguments

res

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 transitionsget, 6. number of possible silent transversions, and 7. whether the position is in a CpG dinucleotide. Is subsetted by a particular gene list to include only genes used for nonsilent rate estimation (see generate.sel.exome)

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

an object of the same structure as res, but columns 3 and 4 (e, and f) have been multiplied by the nonsilent relative rate parameter r.

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.