TotalCnBinnedSmoothing: The TotalCnBinnedSmoothing class

In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

The TotalCnBinnedSmoothing class

Description

Package: aroma.cn
Class TotalCnBinnedSmoothing

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--TotalCnSmoothing
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--TotalCnBinnedSmoothing

Directly known subclasses:

public static class TotalCnBinnedSmoothing
extends TotalCnSmoothing

Usage

TotalCnBinnedSmoothing(..., robust=FALSE)

Arguments

...	Arguments passed to TotalCnSmoothing.
robust	If TRUE, a robust smoother is used, otherwise not.

Details

Note that dsS <- TotalCnBinnedSmoothing(ds, targetUgp=ugp) where ugp <- getAromaUgpFile(ds) returns a data set with an identical set of loci as the input data set and identical signals as the input ones, except for loci with duplicated positions. If all loci have unique positions, the the output is identical to the input.

Fields and Methods

Methods:
No methods defined.

Methods inherited from TotalCnSmoothing:
getAsteriskTags, getOutputDataSet0, getOutputFileClass, getOutputFileExtension, getOutputFileSetClass, getOutputFiles, getParameters, getPath, getRootPath, getTargetPositions, getTargetUgpFile, process, smoothRawCopyNumbers

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

Author(s)

Henrik Bengtsson

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.