MatSmoothing {aroma.affymetrix}R Documentation

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:
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

Author(s)

Mark Robinson (mrobinson[at]wehi.edu.au).


[Package aroma.affymetrix version 1.2.0 Index]