plotColorBias1D: Plot the color bias density plot of Illumina Infinium...

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

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

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.

Value

Invisibly return TRUE if plot successfully.

Author(s)

Pan DU

See Also

See Also as plotColorBias2D and boxplotColorBias

Examples

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

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