calculate.bij: Calculate the background mutation probability for every...

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

Description

This function calcuates the empirical Bayes estimate of a mutation occurring in every gene and sample according to the background mutation model

Usage

  calculate.bij(gid, gene, p, s, epsilon, delta,
    exome.constants.mult, sample.name, muttable,
    nonsil.mut.type, a, b, uniqueA, tableA)

Arguments

gid	a character vector containing the Ensembl gene ids of all genes
exome.constants.mult	an object returned by multiply.p.s.epsilon
sample.name	a character vector containing the names of all samples
muttable	a matrix containing the likelihood due to existing background mutations, see mut.lik.change
nonsil.mut.type	a matrix with one row for every observed mutation, with 10 columns in this order: Ensemble gene id, chromosome, position, mutation type (SNP or In_frame or Frame_shift), reference allele, tumor allele 1, tumor allele 2, sample id, mutation type (1=transition or 2=transversion), and SIFT score
a	numeric value for the maximum likelihood estimate of the hyperparameter a representing the prior for q_j (sample-specific mutation rate, q_j~Unif(a,b))
b	numeric value for the maximum likelihood estimate of the hyperparameter b representing the prior for q_j (sample-specific mutation rate, q_j~Unif(a,b))
uniqueA	a numeric vector containing all unique values of A (see getA)
tableA	a numeric vector of the same length of uniqueA that contains the number of instances of each value in uniqueA
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).
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).

Details

the return value is only calculated for genes with two or more mutations to save on computation time.

Value

a list with one entry for each gene where each entry contains a vector with the probability of mutation for each sample

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.