plotDensity: Log-ratio density plot for all probes and control probes
In charm: Analysis of DNA methylation data from CHARM microarrays

Description Usage Arguments Details Value Author(s) Examples

Make density plots of log-ratios for two-color microarray data. Two plots are produced: one for all probes on the array, and a second for the control probes.

1 2	plotDensity(dat, rx = c(-4, 6), controlIndex = NULL, controlProbes=NULL, pdfFile = NULL, main = NULL, lab=NULL, excludeIndex = NULL)

`dat`	a TilingFeatureSet
`rx`	x-axis range
`controlIndex`	a vector of non-CpG control probe indices
`controlProbes`	vector of names used to denote control probes in the 'container' column of the Nimblegen annotation (ndf) file.
`pdfFile`	name of output pdf file
`main`	main title
`lab`	vector of sample labels. If not specified the sample names from dat will be used.
`excludeIndex`	a numeric vector of probe indices indicating which pm probes to ignore when plotting.

This function makes density plots for a) all probes and b) control probes. It is typically called from within methp when a file name is specified for its plotDensity option. The plots are useful for identifying problematic outlier samples.

No return value. Called for its side-effect of producing a pdf plot.

Martin Aryee <aryee@jhu.edu>

	if (require(charmData) & require(BSgenome.Hsapiens.UCSC.hg18)) {
		phenodataDir <- system.file("extdata", package="charmData")
		pd <- read.delim(file.path(phenodataDir, "phenodata.txt"))
		# Read in raw data
		dataDir <- system.file("data", package="charmData")
		rawData <- readCharm(path=dataDir, files=pd$filename,
			 sampleKey=pd)
		ctrlIdx <- getControlIndex(rawData, subject=Hsapiens)
                ## Not run:
		#plotDensity(rawData, controlIndex=ctrlIdx, pdfFile="density.pdf")	
	}