cpgBoxplots: Boxplots of intensity, binned by Cpg Density

Description

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

Usage

"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))
"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))

Arguments

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.

Value

Invisibly returns a list of the plots.

Details

CpG content of probes is calculated in a 600 base window surrounding the probe, with a linearly decresasing weighting further away from the probe.