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]