plotColorBias2D: Plot the color bias of Illumina Infinium Methylation data in two dimensions

Description

Plot the color bias (red and green channel) of Illumina Infinium Methylation data of one selected sample in two dimensions (methylated and unmethylated probe intensities)

Usage

plotColorBias2D(methyLumiM, selSample = 1, combineMode = F, layoutRatioWidth = c(0.75, 0.25), layoutRatioHeight = c(0.25, 0.75), margins = c(5, 5, 2, 2), cex = 1.25, logMode = TRUE, subset = NULL, ...)

Arguments

methyLumiM

MethyLumiM-class object or eSet-class object, which include methylated and unmethylated probe intensities

selSample

The index of sample name of the selected sample to plot color bias

combineMode

Whether combine two color channels together and plot as one color

layoutRatioWidth

the plot figure ratio between scatter plot and density plot

layoutRatioHeight

the plot figure ratio between scatter plot and density plot

margins

margin of the plot

cex

A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. See par

logMode

Whether plot the intensities in log-scale

subset

plot subset of randomly selected rows. All data will be plotted if it is NULL.

...

other parameters used by plot

Value

Invisibly return TRUE if plot successfully.

Details

The function basically plots the probe intensities in 2-dimension (methylated vs unmethylated), and colors the dots in Red and Green based on their color channel information. The related density plot will also be plotted at the right and top of the scatter plot.

Examples

Run this code

data(example.lumiMethy)
# plot in 2D plot of one selected sample
plotColorBias2D(example.lumiMethy, selSample = 1)