generate.sel.exome: Select the part of exome.constants that belongs to a list of...

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

Description

A function to pull only those base pairs that reside within a list of genes from the object exome.constants

Usage

  generate.sel.exome(genelist, gene, exome.constants)

Arguments

genelist	a vector containing gene names to subset on
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.constants	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.

Value

an object of the same structure as exome.constants, but only containing positions that reside in the genes of genelist

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.