LayoutGroups: The LayoutGroups 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 LayoutGroups

Object
~~|
~~+--LayoutGroups

Directly known subclasses:
GeneGroups, PlateGroups, PrintdipGroups, PrinttipGroups, SlideColumnGroups, SlideRowGroups, SuperGroups

public abstract static class LayoutGroups
extends Object

The LayoutGroups class is a companion class for the Layout class.

1	LayoutGroups(layout=NULL)

layout

A Layout object specifying the layout of a set of microarrays.

Methods:

	`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 LayoutGroups.

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)