MatSmoothing: The MatSmoothing class

Description

Package: aroma.affymetrix Class MatSmoothing Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--MatSmoothing Directly known subclasses: public static class MatSmoothing extends ProbeLevelTransform This class represents a function for smoothing data with a trimmed mean.

Usage

MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)

Arguments

...

Arguments passed to ProbeLevelTransform.

design

A design matrix.

probeWindow

Bandwidth to use. Effectively the width is 2*probeWindow since it looks probeWindow bases in either direction.

nProbes

The minimum number of probes to calculate a MAT score for.

meanTrim

The amount of trimming of the mean in [0,0.5].

Fields and Methods

Methods: rll{ process Processes the data set. }

Methods inherited from ProbeLevelTransform: getRootPath

Methods inherited from Transform: getOutputDataSet, getOutputFiles

Methods inherited from AromaTransform: as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags

Methods inherited from ParametersInterface: getParameterSets, getParameters, getParametersAsString

Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis