exportPlot: Export plots to pdf files.

In carter-allen/dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Description

Exports the plots of estimated binding sites (plotType="fit") or the goodness of fit (GOF) plots (plotType="GOF") to a PDF file.

Usage

exportPlot(x, y, ...)

Arguments

x	Object of class DpeakFit

,

y	Name of file to export to.
...	Other parameters to be passed through to generic exportPlot.

Details

Exports the plots of estimated binding sites (plotType="fit") or the goodness of fit (GOF) plots (plotType="GOF") to a PDF file. Its file name needs to be specified in the filename argument. In both of these plots, estimated binding sites or simulated fragments are superimposed on the plots of reads (or fragments) aligned to each position. For SET data, if plotType="fit" and strand=TRUE, reads will be plotted in a strand-specific manner, where each read is extended to extension from its 5' end. If smoothing=TRUE, a smoothed plot (using the smoothing spline) is provided. Unsmoothed plot is provided by default.

Value

Export plots to files

Author(s)

Dongjun Chung

Examples

data(exampleData)
exampleFit <- dpeakFit( exampleData, maxComp=5)
exportPlot( exampleFit, filename="exampleResult_combined.pdf" )

carter-allen/dpeak documentation built on April 23, 2020, 4:09 p.m.