ScanCBSPlot: Main Plotting of the scan statistic segmentation
In seqCBS: Copy Number Profiling using Sequencing and CBS

Description Usage Arguments Details Value Author(s) See Also

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

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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 `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

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

seqCBS documentation built on May 2, 2019, 9:15 a.m.