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

In cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

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

cancerTiming documentation built on May 2, 2019, 9:28 a.m.