Description Usage Arguments Details Value Author(s) See Also
This is an overall plotting function to display the segmentation for a chromosome
1 2 3 | 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)
|
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 |
filename |
The output file names of the plot |
mainTitle |
The title of the plot |
CIObj |
Optional; the Bayesian CI computed by |
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 |
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.
No return object
Jeremy J. shen
ScanCBS
, ScanCBSSimPlot
, relCNComp
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