mut.type.converter: Get total counts of mutations for each replication timing,...

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

Description

This function reads in a mutation table and returns the total counts of mutations in each of the replication timing regions, expression level categories, and mutation types. It also returns a reformatted mutation table.

Usage

  mut.type.converter(mutab, exome.SIFT, seq.in.chrom,
    dCG.in.chrom, gene)

Arguments

seq.in.chrom	a list with an item for each chromosome that contains a matrix whose first column is the position and the second column is the nucleotide of a base pair within that chromosomes (first item returned from preprocess.BM)
dCG.in.chrom	a list with an item for each chromosome that contains a vector of the position of the CpG dinucleotide coding sequences (second item returned from preprocess.BM)
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.
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).
exome.SIFT	list object with one item per chromosome where each item contains matrix with one row per coding base pair and 7 columns: position, nucleotide, CpG context, FI score for mutation to "A", FI score for mutation to "C", FI score for mutation to "G", and FI score for mutation to "T".

Value

a list object with two elements:

mut.per.type.sum	a 3 by 3 by 6 matrix with the total counts of mutations in each of the 3 replication timing regions, 3 expression level categories, and 6 mutation types (indels counted separately since every base pair is at risk for this type of mutation).
mutab	a reformatted mutation table that contains an extra two columns: 1. a mutation type indicator (1= transition, 2=transversion, and 3=indel), 2. SIFT score for the mutation.

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.