This is an overall plotting function to display the segmentation for a chromosome
ScanCBSPlot(cases, controls, CBSObj, filename, mainTitle, CIObj=NULL,
length.out=10000, localWindow=0.5*10^5, localSeparatePlot=TRUE,
smoothF=0.025, xlabScale=10^6, width=12, height=18)The case read positions (should be restricted to a chromosome)
The control read positions (should be restricted to a chromosome)
The output object of the ScanCBS function
The output file names of the plot
The title of the plot
Optional; the Bayesian CI computed by BayesCptCI function
The number of windows to use for the display of smoothed rate estimates
The number of genome locations to show around each of the called change points
Whether to show the local behavior of each change point in a seperate PDF file. Default to TRUE. The output file are the given filename attached with the index and actual location of the change point.
The lowess smoothing factor. The proportion of windows around the current window that affects its smoothed rate estimate
The scaling factor of the read positions, often in 10^6, or Mb
The width of the output graph in inches
The height of the output graph in inches
No return object
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. It also makes a zoom-in plot for a region around each of the called change points.