discontPlot: Plot with discontinuous smoother

In CAFE: Chromosmal Aberrations Finder in Expression data

Description

Plots chromosome plots with a discontinuous smoother

Usage

discontPlot(datalist,samples=c(1,2),chromNum=1,gamma=300,idiogram=FALSE,
file="default")

Arguments

datalist	The CAFE datalist to be analyzed, i.e. the output of ProcessCels.
samples	A vector or sample numbers to be plotted
chromNum	the chromosome to be plotted
gamma	The gamma level can be roughly compared to the sliding window size in a normal continuous smoother. The gamma level determines how strict the algorithm functions; a higher level will correspond to fewer jumps. This can not be higher than the total number of probesets on the to-be-analyzed chromosome. Must be a positive integer.
idiogram	if TRUE, will overlay a chromosome idiogram over the chromosome plot
file	Specify a file name to store output png file

Value

Plot to file system; Returns a ggplot2 graph if chromNum!="ALL". When chromNum=="ALL", returns a list of ggplot2 graphs.

Author(s)

Sander Bollen

References

Friedrich, F., Kempe, a, Liebscher, V., & Winkler, G. (2008). Complexity Penalized M-Estimation. Journal of Computational and Graphical Statistics, 17(1), 201-224. doi:10.1198/106186008X285591

See Also

rawPlot slidPlot facetPlot

Examples

data("CAFE_data")
discontPlot(CAFE_data,samples=9,chromNum=17,gamma=300)

CAFE documentation built on Nov. 8, 2020, 7:44 p.m.