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

Description Usage Arguments Fields and Methods Author(s) Examples

Package: aroma
Class GeneGroups

Object
~~|
~~+--LayoutGroups
~~~~~~~|
~~~~~~~+--GeneGroups

Directly known subclasses:

public abstract static class GeneGroups
extends LayoutGroups

1	GeneGroups(layout=NULL, specification=NULL)

`layout`	A Layout object.
`specification`	(optional) `character` string specifying what type of within-slide replication the slides are printed with. If `NULL`, the within-slide replication will be extracted from the names or the ids of the Layout object. Possible values are `"none"` (no within-slide replications), `"neighboring-pairs"` (duplicated horizontal neighboring pairs) and `"top-bottom"` (duplicated pairs over replicated tiles).

Methods:

	`as.character`	-
	`getDuplicates`	Gets all duplicated spots.
	`getNames`	Gets the names of the unique gene names.
	`getQuadruplicates`	Gets all quadruplicated spots.
	`getReplicates`	Gets all spots that exist with a certain number of replicates.
	`getSizes`	Gets the number of replicates for each gene.
	`getSpots`	Gets a list of items each containing spot indices for a group.
	`getTriplicates`	Gets all triplicated spots.
	`nbrOfGroups`	Gets the number of unique genes.

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/)

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)