MatSmoothing: The MatSmoothing class

Description

Package: aroma.affymetrix Class MatSmoothing Object ~~| ~~+--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 Transform: getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles Methods inherited from AromaTransform: getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags Methods inherited from Object: asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save