ScanAlyze20Data: The ScanAlyze20Data (ScanAlyze v2.0) class
In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description Usage Arguments Fields and Methods Author(s) References

Package: aroma
Class ScanAlyze20Data

Object
~~|
~~+--MicroarrayData
~~~~~~~|
~~~~~~~+--ScanAlyzeData
~~~~~~~~~~~~|
~~~~~~~~~~~~+--ScanAlyze20Data

Directly known subclasses:

public static class ScanAlyze20Data
extends ScanAlyzeData

Creates an empty ScanAlyze20Data object.

1	ScanAlyze20Data(layout=NULL)

layout

A Layout object specifying the spot layout of the slides in this data set.

Methods:

	`getArea`	-
	`getBackground`	-
	`getBackgroundSD`	-
	`getBgArea`	-
	`getDiameter`	-
	`getForeground`	-
	`getForegroundSD`	-
	`getGrid`	-
	`getSpotColumn`	-
	`getSpotPosition`	Gets physical positions of the spots.
	`getSpotRow`	-
	`read`	Reads one or several ScanAlyze v2.0 files.
	`write`	Writes a ScanAlyze v2.0 Results Data file (NOT IMPLEMENTED).

Methods inherited from ScanAlyzeData:
append, as.RawData, getArea, getBackground, getBgArea, getCircularity, getDiameter, getForeground, getGrid, getRawData, getSpotColumn, getSpotPosition, getSpotRow, normalizeGenewise, plotSpatial, plotSpatial3d, read, write

Methods inherited from MicroarrayData:
addFlag, append, applyGenewise, applyGroupwise, applyPlatewise, applyPrintdipwise, applyPrinttipwise, as.character, as.data.frame, boxplot, clearCache, clearFlag, createColors, dataFrameToList, equals, extract, getBlank, getCache, getChannelNames, getColors, getExcludedSpots, getExtra, getExtreme, getFieldNames, getFlag, getInclude, getLabel, getLayout, getProbeWeights, getSignalWeights, getSlideNames, getSlidePairs, getSpotPosition, getSpotValue, getTreatments, getView, getWeights, getWeightsAsString, hasExcludedSpots, hasLayout, hasProbeWeights, hasSignalWeights, hasWeights, highlight, hist, isFieldColorable, keepSlides, keepSpots, listFlags, lowessCurve, nbrOfDataPoints, nbrOfFields, nbrOfSlides, nbrOfSpots, nbrOfTreatments, normalizePlatewise, normalizePrintorder, normalizeQuantile, plot, plotDensity, plotGene, plotPrintorder, plotReplicates, plotSpatial, plotSpatial3d, plotXY, points, putGene, putSlide, qqnorm, quantile, range, range2, read, readHeader, readToList, removeSlides, removeSpots, resetProbeWeights, resetSignalWeights, select, seq, setCache, setExcludedSpots, setExtra, setFlag, setLabel, setLayout, setProbeWeights, setSignalWeights, setSlideNames, setTreatments, setView, setWeights, size, str, subplots, summary, text, updateHeader, validateArgumentChannel, validateArgumentChannels, validateArgumentGroupBy, validateArgumentSlide, validateArgumentSlides, validateArgumentSpotIndex, validateArgumentWeights, write, 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/)

[1] http://array.mbb.yale.edu/analysis/manual/inputfiles/

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