plotColorBias1D: Plot the color bias density plot of Illumina Infinium Methylation data

Description

Plot the color bias density plot of Illumina Infinium Methylation data in one dimension (comparing with 2D scatter plot)

Usage

plotColorBias1D(methyLumiM, channel = c("both", "unmethy", "methy", "sum"), colorMode=TRUE, removeGenderProbes = FALSE, logMode = TRUE, subset = NULL, ...)

Arguments

methyLumiM

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

channel

estimate the intensity in different methods

colorMode

whether separate two color channels or not

removeGenderProbes

determine whether exclude probes on X and Y chromosomes if the chromosome information is provided in the methyLumiM object.

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 density and plot

Value

Invisibly return TRUE if plot successfully.

Details

Plot the color bias density plot of Illumina Infinium Methylation data. There are four options using "channel" parameter to plot the density plot. "both": estimate the density by pooling together methylated and unmethylated probe intensities. "unmethy" and "methy": plot either unmethylated or methylated probe density. "sum" plot the density of the sum of methylatled and unmethylated probe intensitys.

Examples

Run this code

data(example.lumiMethy)
# before adjustment
plotColorBias1D(example.lumiMethy)