Main Plotting of the scan statistic segmentation

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Description

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

Usage

1
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)

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

CIObj

Optional; the Bayesian CI computed by BayesCptCI function

length.out

The number of windows to use for the display of smoothed rate estimates

localWindow

The number of genome locations to show around each of the called change points

localSeparatePlot

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.

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. It also makes a zoom-in plot for a region around each of the called change points.

Value

No return object

Author(s)

Jeremy J. shen

See Also

ScanCBS, ScanCBSSimPlot, relCNComp

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