fit.background.model: Fit background mutation model

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

Description

This function calculates the relative rate parameters of the background mutation model, estimated by method of moments

Usage

  fit.background.model(mutab, nonsil.mut.type.sampl.sum,
    sil.mut.type.sampl.sum, nonsil.type.const,
    sil.type.const, gene)

Arguments

mutab	a matrix containing one row per mutation and 8 columns (Ensembl gene name, chromosome, position, variant type (SNP, In_frame, Frame_shift), reference allele, tumor allele 1, tumor allele 2, and sample id.
nonsil.mut.type.sampl.sum	a 3 (expression category) by 3(replication timing category) by 6 (mutation type) matrix containing the total number of base pairs eligible for a nonsilent mutation in each category (2nd item obtained from mut.type.converter)
sil.mut.type.sampl.sum	a 3 (expression category) by 3(replication timing category) by 6 (mutation type) matrix containing the total number of base pairs eligible for a silent mutation in each category (2nd item obtained from mut.type.converter)
nonsil.type.const	list of 3 objects with information about nonsilent coding sequences (see preprocess.BM)
sil.type.const	list of 3 objects with information about silent coding sequences (see preprocess.BM)
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 list object with four elements:

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.
r	numeric value representing the relative rate parameter estimate for the ratio of mutations in genes with nonsilent vs only silent mutations (selection bias)
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 containing the relative rate parameters for the three expression levels (1=Low, 2=Medium, 3=High)
delta	a 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).

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.