boxplotBeads {beadarray} | R Documentation

## Box plot of bead intensities

### Description

Function to produce box plots of the bead intensities from different bead arrays

### Usage

    boxplotBeads(BLData, whatToPlot = "G", arrays = NULL, log = TRUE,
              varwidth = TRUE, method = "illumina", n = 3, trim = 0.05, ...)

### Arguments

`BLData` | a BeadLevelList object
`whatToPlot` | character string specifying which intensities to plot. See `getArrayData` for a list of the possibilities.
`arrays` | numeric vector of arrays to plot
`log` | if TRUE log2 intensities are plotted
`varwidth` | logial, indicating whether box widths should be proportional to the number of values in each box plot
`method` | chracter string specifying the summarisation method to use (only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`). Refer to help `createBeadSummaryData` help page for further information.
`n` | use n median absolute deviations from the median as a cut-off for outliers. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to help `createBeadSummaryData` help page for further information.
`trim` | fraction of intensities to remove from the bead summary calculations. Only applicable when `whatToPlot="residG"`, `"residR"` or `"residM"`. Refer to `createBeadSummaryData` help page for further information.
`...` | further graphical parameters to the `boxplot` function from the graphics package

### Details

Produces box plots of the raw intensities from a bead array

### Value

Plot is produced on current graphical device

### Author(s)

Matt Ritchie

### Examples

    data(BLData)

    boxplotBeads(BLData)

[Package beadarray version 1.6.0 Index]