beadarrayMSV (version 1.0.3)

scatterArrays: Cartesian scatter-plots of two-colour intensities

Description

Scatter-plots for a series of arrays are produced. Which intensities are plotted depends on whether the input BSData is an instance of "BeadSetIllumina" or "AlleleSetIllumina"

Usage

scatterArrays(BSData, arrays, markers = seq(1, nrow(BSData), 5),
    smooth = TRUE, newFigure = TRUE, maxPlots = 72, ...)

Arguments

BSData

"BeadSetIllumina" object (intensities G vs. R are plotted) or "AlleleSetIllumina" object (intensities B vs.

arrays

Indexes to arrays

markers

Indexes to markers

smooth

If TRUE, density-plots are used (see smoothScatter)

newFigure

Logical indicating whether or not to clear the current device before plotting. If FALSE, an error will be produced if more than one array is specified.

maxPlots

Numeric indicating the maximum allowed number of arrays to plot. Exceeding this limit will produce an error.

...

Additional graphical input parameters

Value

• This function is called for its side effects

See Also

BeadSetIllumina, AlleleSetIllumina, plotPreprocessing, plotGenotypes

Examples

#Read a BeadSetIllumina object using files in example data directory
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)

## Plot G vs. R
dev.new()
scatterArrays(BSDataRaw,smooth=FALSE)