GalLayout: Class representing GenePix Array List (GAL) data
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

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

Package: aroma
Class GalLayout

Object
~~|
~~+--Layout
~~~~~~~|
~~~~~~~+--GalLayout

Directly known subclasses:

public static class GalLayout
extends Layout

1	GalLayout(...)

...

Arguments accepted by the Layout constructor.

Methods:

	`as.data.frame`	-
	`getBlock`	-
	`getColumn`	-
	`getFieldNames`	-
	`getGridColumn`	-
	`getGridRow`	-
	`getRow`	-
	`nbrOfFields`	-
	`read`	Reads a GenePix Array List (GAL) file.
	`write`	-

Methods inherited from Layout:
anonymize, as.character, as.data.frame, as, as.Layout, equals, fromDataFrame, getBlank, getGeneGroups, getId, getIndex, getIndices, getLayoutGroupsByName, getLocation, getName, getPlate, getPlateGroups, getPlateNumber, getPosition, getPrintdipGroups, getPrintorder, getPrinttipGroups, getSlideColumnGroups, getSlideRowGroups, gridSize, hasIds, hasNames, hasPlates, indexOf, nbrOfColumns, nbrOfGrids, nbrOfPlates, nbrOfReplicates, nbrOfRows, nbrOfSpots, put, read, rename, set, setGeneGroups, setId, setName, setPlate, setPlateGroups, setPrintdipGroups, setPrintorder, setPrinttipGroups, setSlideColumnGroups, setSlideRowGroups, size, toXYMatrix, write

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/)

The GenePix Array List (GAL) file format, http://www.axon.com/GN_GenePix_File_Formats.html.

The superclass Layout.

 ## Not run: 
  layout <- GalLayout$read("fish.gal")
  genes <- getGeneGroups(layout)
  print(genes)
 
## End(Not run)

 ## Not run: 
  # Gives:
   [1] "GeneGroups: 7769 groups defined. 7680 genes with 1 replicates, 75
   genes with 3 replicates, 5 genes with 6 replicates, 4 genes with 16
   replicates, 4 genes with 64 replicates, 1 genes (3XSSC) with 193
   replicates."
 
## End(Not run)