scatterArrays: Cartesian scatter-plots of two-colour intensities

Description Usage Arguments Value Author(s) See Also Examples

View source: R/beadarrayMSV.R

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

1
2
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. “A” are plotted)

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

Author(s)

Lars Gidskehaug

See Also

BeadSetIllumina, AlleleSetIllumina, plotPreprocessing, plotGenotypes

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
## Not run: 
#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)

## End(Not run)

beadarrayMSV documentation built on May 29, 2017, 9:07 a.m.