plotSeqCount {cancerTiming}R Documentation

Basic function for plotting the ratio of tumor to normal coverage

Description

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.

Usage

plotSeqCount(position, t_count, n_count, ylim=NULL, normFac=1, 
	segs, segColors = palette(), ...)

Arguments

position

vector of position of the base

t_count

vector of number of reads overlapping position in tumor

n_count

vector of number of reads overlapping position in normal

ylim

set the limits of y axis. If NULL, default values found.

normFac

a normalizing factor to correct for

segs

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

segColors
...

passed to plot

Author(s)

Elizabeth Purdom


[Package cancerTiming version 3.1.8 Index]