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

Description Fields and Methods Author(s)

Package: aroma
Class MicroarrayData

Object
~~|
~~+--MicroarrayData

Directly known subclasses:
BMAData, GenePixData, ImaGeneData, MAData, QuantArrayData, RawData, RGData, ScanAlyze20Data, ScanAlyzeData, SpotData, SpotfinderData, TMAData

public static class MicroarrayData
extends Object

This class is abstract can not be instanciated.

Fields

	`layout`	The layout structure of the microarray slide(s).

Methods:

	`append`	Appends another MicroarrayData object.
	`applyGenewise`	-
	`applyGroupwise`	-
	`applyPlatewise`	-
	`applyPrintdipwise`	-
	`applyPrinttipwise`	-
	`as.character`	-
	`as.data.frame`	Converts the object to a data frame.
	`boxplot`	Plots a boxplot.
	`clearCache`	-
	`equals`	Compares a MicroarrayData object with another Object.
	`extract`	Gets a subset of data specified by fields, slides and/or spot indices.
	`getBlank`	-
	`getCache`	-
	`getChannelNames`	Gets the names of the channels.
	`getColors`	-
	`getExtreme`	-
	`getInclude`	-
	`getLabel`	Gets the label of one field.
	`getLayout`	Gets the layout.
	`getProbeWeights`	-
	`getSignalWeights`	-
	`getSlideNames`	Gets the names of the slides.
	`getSlidePairs`	-
	`getSpotPosition`	-
	`getSpotValue`	-
	`getTreatments`	-
	`getView`	-
	`getWeights`	-
	`getWeightsAsString`	-
	`hasLayout`	Checks if the layout has been specified.
	`hasProbeWeights`	-
	`hasSignalWeights`	-
	`hasWeights`	-
	`highlight`	Highlight spots in last plot.
	`hist`	Plots a histogram.
	`isFieldColorable`	-
	`keepSlides`	Remove all but the specified slides.
	`keepSpots`	Remove all but the specified spots from all slides.
	`lowessCurve`	Draws one or more lowess curves through the data in last plot.
	`nbrOfDataPoints`	-
	`nbrOfFields`	Gets the number of fields.
	`nbrOfSlides`	Gets the number of slides.
	`nbrOfSpots`	Gets the number of spots in each of the slides.
	`nbrOfTreatments`	-
	`normalizePlatewise`	Normalization performed plate by plate.
	`normalizePrintorder`	-
	`normalizeQuantile`	-
	`plot`	Plots spatial representation of a microarray spot statistics.
	`plotDensity`	Plots the empirical density distribution of a field.
	`plotGene`	-
	`plotPrintorder`	Plots the data as a time series in the order it was printed.
	`plotReplicates`	-
	`plotSpatial`	Plots a spatial representation of one field.
	`plotSpatial3d`	Plots a 3-dimensional spatial representation of a field.
	`plotXY`	Plots a scatter plot of two fields.
	`points`	-
	`qqnorm`	-
	`quantile`	-
	`range`	-
	`range2`	-
	`read`	Reads microarray data generated by another software package.
	`readHeader`	-
	`removeSlides`	Remove specified slides.
	`removeSpots`	Remove specified spots.
	`resetProbeWeights`	-
	`resetSignalWeights`	-
	`select`	Selects rows with certain criteria.
	`seq`	-
	`setCache`	-
	`setLabel`	Sets the label of one field.
	`setLayout`	Sets the layout.
	`setProbeWeights`	Sets probe weights on one or several slides.
	`setSignalWeights`	-
	`setSlideNames`	Sets the names of the slides.
	`setTreatments`	-
	`setView`	-
	`setWeights`	-
	`size`	Gets the number of spots in all slides together.
	`str`	Compactly Display the Structure of a MicroarrayData object.
	`subplots`	Prepare for a grid of subplots based on the number of slides.
	`summary`	Gets summary statistics for the fields.
	`text`	Puts labels to the spots in last plot.
	`updateHeader`	-
	`validateArgumentChannel`	-
	`validateArgumentChannels`	-
	`validateArgumentGroupBy`	Validates the argument 'groupBy'.
	`validateArgumentWeights`	Validates the argument 'weights'.
	`write`	Write a MicroarrayData object to file.
	`writeHeader`	-

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/)

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.