cpgBoxplots {Repitools} | R Documentation

## 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

    ## 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))

### 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.

### 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.

### Value

Invisibly returns a list of the plots.

### Author(s)

Mark Robinson, Dario Strbenac

[Package Repitools version 1.26.0 Index]