MatSmoothing: The MatSmoothing class
In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

MatSmoothing

R Documentation

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].

Details

This class requires the gsmoothr package, which was archived on CRAN in May 2025.

Fields and Methods

Methods:

	`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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis