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.
MatSmoothing(..., design=NULL, probeWindow=300, nProbes=10, meanTrim=0.1)
Arguments passed to ProbeLevelTransform.
A design matrix.
Bandwidth to use. Effectively the width is 2*probeWindow since it looks probeWindow bases in either direction.
The minimum number of probes to calculate a MAT score for.
The amount of trimming of the mean in [0,0.5].
Methods:
process | - |
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
Mark Robinson, Henrik Bengtsson