slidPlot: Plot with sliding average smoother

In CAFE: Chromosmal Aberrations Finder in Expression data

Description

Plots chromosome plots with a moving average smoother

Usage

slidPlot(datalist,samples=c(1,2),chromNum=1,combine=FALSE,k=1,idiogram=FALSE,file="default")

Arguments

datalist	The CAFE datalist to be analyzed, i.e. the output of ProcessCels.
samples	A vector of sample numbers to be plotted
chromNum	The chromosome to be analyzed
combine	If TRUE, will plot the unaltered raw data in the background
k	The sliding window size. Must be a positive integer, smaller than the total number of probesets on the chromosome
idiogram	If TRUE, will plot a chromosome idiogram over the plot
file	Specify a file name to store output png fileS

Value

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

Note

Makes heavy use of the ggplot2 package.

Author(s)

Sander Bollen

References

H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009.

See Also

rawPlot facetPlot discontPlot

Examples

data("CAFE_data")
slidPlot(CAFE_data,samples=9,chromNum=17,k=50,combine=TRUE)

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