MEDIPS.plotCalibrationPlot: Creates the calibration plot.

In chavez-lab/MEDIPS: DNA IP-seq data analysis

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.

Author(s)

Lukas Chavez, Matthias Lienhard

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)

chavez-lab/MEDIPS documentation built on Feb. 17, 2021, 3:24 a.m.