PlateGroups: The PlateGroups class
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Fields and Methods Author(s) See Also Examples

Package: aroma
Class PlateGroups

Object
~~|
~~+--LayoutGroups
~~~~~~~|
~~~~~~~+--PlateGroups

Directly known subclasses:

public abstract static class PlateGroups
extends LayoutGroups

1	PlateGroups(layout=NULL, plateDef=NULL)

`layout`	A `Layout` object specifying the layout of a set of microarrays.
`plateDef`	If a scalar (`numeric` of length one), each plate group is assumed to contain that number of spots/clones. Can also be a `data.frame`. If `NULL`, the plates are obtained from the Layout object, which then is required to contain plate information.

Methods:

	`as.character`	-
	`getFirst`	-
	`getLast`	-
	`getNames`	-
	`getPrintorderIndices`	-
	`getSizes`	-
	`getSpots`	-
	`nbrOfGroups`	-

Methods inherited from LayoutGroups:
apply, as.character, getGroupValues, getLayout, getNames, getSpots, getSpotValues, nbrOfGroups, seq, setLayout

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save

Henrik Bengtsson (http://www.braju.com/R/)

For more information see PlateGroups.

layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))

# Extract the printtip groups
printtips <- PrinttipGroups(layout)
print(printtips)

# Extract the plate groups (using getPlate(layout))
plates <- PlateGroups(layout)
print(plates)

# Extract the (within-slide) replicate groups (using getName/ID(layout))
replicates <- GeneGroups(layout)
print(replicates)

# Define the (within-slide) replicate groups
duplicates <- GeneGroups(layout, "neighboring-pairs")
print(duplicates)