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

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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

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.

Value

Invisibly return TRUE if plot successfully.

Author(s)

Pan DU

See Also

See Also as plotColorBias1D

Examples

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

lumi documentation built on Nov. 8, 2020, 5:27 p.m.