plotSeqCount:
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