Description Usage Arguments Details Value Author(s) See Also
View source: R/ScanCBSSimPlot.R
This is an overall plotting function to display the segmentation for a chromosome, for simulation data.
1 | ScanCBSSimPlot(cases, controls, CBSObj, trueTau, SpikeMat, filename, mainTitle, length.out=1000, smoothF=25, xlabScale=10^6, width=12, height=9)
|
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 |
trueTau |
The true location of the change points in simulation |
SpikeMat |
The matrix of signal spikes as generated by the relevant simulation functions |
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 |
This is similar to ScanCBSPlot
. 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
No return object
Jeremy J. Shen
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.