cpgBoxPlots: Boxplots of intensity, binned by Cpg Density

In markrobinsonuzh/Repitools: Epigenomic tools

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

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.