boxplotBeads {beadarray}R Documentation

Box plot of bead intensities

Description

Function to produce box plots of the bead intensities from selected strips/arrays from a BeadLevelList object.

Usage

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

Arguments

BLData BeadLevelList
whatToPlot character string specifying which intensities to plot. See getArrayData for a list of the possibilities.
arrays integer (scalar or vector) specifying the strips/arrays to plot. If NULL, all the strips/arrays are plotted.
log if TRUE log2 intensities are plotted
varwidth logical, indicating whether box widths should be proportional to the number of values in each box plot
method character 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 numeric value defining a cut-off for the number of median absolute deviations (MADs) from the median to use for determining outliers. The default value is 3. Only applicable when whatToPlot="residG", "residR" or "residM" and method="illumina". 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 specified intensities for selected strips/arrays.

Value

A plot is produced on the current graphical device

Author(s)

Matt Ritchie

Examples

data(BLData)

boxplotBeads(BLData)

[Package beadarray version 1.10.0 Index]