preprocess.BM: Pull out sequences, CpG dinucleotide positions, and base...

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

Description

A function to gather information about a given gene list that will be needed to fit the background mutation model. It pulls out the sequence of the genes in the list X, as well as indicates which of the positions resides in a CpG dinucleotide pair, and counts how many base pairs are at risk for mutation in the 108 combinations of 6 mutation types x 2 silent/nonsilent status x 3 replication timing categories x 3 expression level categories.

Usage

  preprocess.BM(X, gene)

Arguments

X

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 transitions, 6. number of possible silent transversions, and 7. whether the position is in a CpG dinucleotide. May be subsetted by a particular gene list (see generate.sel.exome)

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 with three items:

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
dCG.in.chrom	position of the CpG dinucleotide coding sequences within chromosomes
type.const	a 3 by 12 matrix containing E_1,n,h,F_2,n,h,E_3,n,h,F_4,n,h,E_5,n,h,F_6,n,h, C_1,n,h,D_2,n,h,C_3,n,h,D_4,n,h,C_5,n,h,D_6,n,h for n=1,2,3, and h=1,2,3

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.