plotSeqCount

position

vector of number of reads overlapping position in tumor

t_count

vector of number of reads overlapping position in normal

n_count

normFac

factor as same length as position, identifying which segment a count is from

segs

segColors

Basic function for plotting the ratio of tumor to normal coverage, and calculating the average over segments. A simple tool for assessing copy number breaks.

This is a package with functions for timing copy number
        changes using estimates of mutational allele frequency from
        resequencing of tumor samples.

plotSeqCount: Basic function for plotting the ratio of tumor to normal coverage

Description

Usage

Arguments