MEDIPS (version 1.22.0)

MEDIPS.plotCalibrationPlot: Creates the calibration plot.

Description

Visualizes the dependency between MeDIP-seq signals and CpG densities together with the calcibration curve and the results of the linear modelling.

Usage

MEDIPS.plotCalibrationPlot(MSet=NULL, ISet=NULL, CSet=NULL, plot_chr="all", rpkm=T, main="Calibration plot", xrange=T)

Arguments

MSet

a MEDIPS SET object

ISet

an INPUT SET (i.e. a MEDIPS SET created from Input sequening data)

CSet

an according COUPLING SET object

plot_chr

default="all". It is recommended to call a graphics device (e.g. png("calibrationPlot.png")) before calling the plot command, because R might not be able to plot the full amount of data in reasonable time.

rpkm

can be either TRUE or FALSE. If set to TRUE, the methylation signals will be transformed into rpkm before plotted. The coupling values remain untouched. It is necessary to set rpkm=T, if both, a MSet and an ISet are given and plotted at the same time.

main

The title of the calibration plot.

xrange

The signal range of the calibration curve typically falls into a low signal range. By setting the xrange parameter to TRUE, the calibration plot will visualize the low signal range only.

Value

The calibration plot will be visualized.

Examples

library(MEDIPSData)
data(hESCs_MeDIP)
data(CS)

MEDIPS.plotCalibrationPlot(CSet=CS, main="Calibration Plot", MSet=hESCs_MeDIP[[1]], plot_chr="chr22",  rpkm=TRUE,  xrange=TRUE)