cpgBoxPlots: Boxplots of intensity, binned by Cpg Density
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s)

Either makes a side by side boxplot of two designs, or plots a single boxplot for the difference between the two designs.

## S4 method for signature 'AffymetrixCelSet'
cpgBoxplots(this, samples=c(1,2), subsetChrs="chr[1-5]", gcContent=7:18, calcDiff=FALSE, verbose=FALSE, nBins=40, pdfFile=NULL, ylim=if (calcDiff) c(-5,6) else c(4,15), col=if (calcDiff) "salmon" else c("lightgreen","lightblue"), mfrow=if (!is.null(pdfFile)) c(2,2) else c(1,1))
## S4 method for signature 'matrix'
cpgBoxplots(this, ndfTable = NULL, organism, samples=c(1,2), subsetChrs="chr[1-5]", gcContent=7:18, calcDiff=FALSE, verbose=FALSE, nBins=40, pdfFile=NULL, ylim=if (calcDiff) c(-5,6) else c(4,15), col=if (calcDiff) "salmon" else c("lightgreen","lightblue"), mfrow=if (!is.null(pdfFile)) c(2,2) else c(1,1))

`this`	Either an AffymetrixCelSet or a matrix of intensity data.
`ndfTable`	In the case of Nimblegen data, a `data.frame` with at least columns `chr` and `sequence`. Must be in the same order of rows as the intensity data.
`organism`	The `BSgenome` object of the genome build to use for getting DNA sequence surrounding the probes.
`samples`	Which 2 columns from the data matrix to use.
`subsetChrs`	Which chromosomes to limit the analysis to.
`gcContent`	A range of GC content, which only probes that have GC content in the range are used for the graphing.
`calcDiff`	Boolean. Plot the difference between the two samples ?
`verbose`	Boolean. Print processing output.
`nBins`	Bins to bin the intensities into.
`pdfFile`	Name of file to output plots to.
`ylim`	Y limit of graphs
`col`	Colour of boxes.
`mfrow`	Not specified by the user. Rows and columns to draw the plots in.