plotColorBias1D {lumi} | R Documentation

## 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`

### 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)

[Package lumi version 2.44.0 Index]