boxplotBeads {beadarray} | R Documentation |
Function to produce box plots of the bead intensities from
selected strips/arrays from a BeadLevelList
object.
boxplotBeads(BLData, whatToPlot = "G", arrays = NULL, log = TRUE, varwidth = TRUE, method = "illumina", n = 3, trim = 0.05, ...)
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 |
Produces box plots of the specified intensities for selected strips/arrays.
A plot is produced on the current graphical device
Matt Ritchie
data(BLData) boxplotBeads(BLData)