getA: Compute A - the likelihood of a mutation at every position

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

Description

This function computes the likelihood of a mutation occurring at each position in the exome according to the background mutation model

Usage

  getA(nonsil.exclus, sil.exclus, both, p, r, s, epsilon,
    delta, gene)

Arguments

nonsil.exclus	oject obtained from generate.sel.exome representing the exclusively nonsilent genes
sil.exclus	oject obtained from generate.sel.exome representing the exclusively silent genes
both	oject obtained from generate.sel.exome representing the genes with nonsilent mutations also used for silent mutation detection
r	numeric value representing the relative rate parameter estimate for the ratio of mutations in genes with nonsilent vs only silent mutations (selection bias)
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

a numeric vector containting the likelihood of a mutation at every position.

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.