ScanCBSPlot: Main Plotting of the scan statistic segmentation

In SeqCNVCBS: Scan Statistics for CNV Detection with CBS

Description

This is an overall plotting function to display the segmentation for a chromosome

Usage

ScanCBSPlot(cases, controls, CBSObj, filename, mainTitle, length.out = 1000, smoothF = 25, xlabScale = 10^6, width = 12, height = 18)

Arguments

cases	The case read positions (should be restricted to a chromosome)
controls	The control read positions (should be restricted to a chromosome)
CBSObj	The output object of the ScanCBS function
filename	The output file names of the plot
mainTitle	The title of the plot
length.out	The number of windows to use for the display of smoothed rate estimates
smoothF	The lowess smoothing factor. The proportion of windows around the current window that affects its smoothed rate estimate
xlabScale	The scaling factor of the read positions, often in 10^6, or Mb
width	The width of the output graph in inches
height	The height of the output graph in inches

Details

This function produces three sub-graphs, showing the segmentation calls, the smoothed rate estimate, and the inferred relative copy number. It is crucial that one seperates the plot for each chromosome

Value

No return object

Author(s)

Jeremy J. shen

See Also

ScanCBS, relCNComp

SeqCNVCBS documentation built on May 2, 2019, 6:51 p.m.