Package: aroma.cn
Class TotalCnBinnedSmoothing
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--TotalCnSmoothing
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--TotalCnBinnedSmoothing
Directly known subclasses:
public static class TotalCnBinnedSmoothing
extends TotalCnSmoothing
TotalCnBinnedSmoothing(..., robust=FALSE)
Arguments passed to TotalCnSmoothing.
If TRUE, a robust smoother is used, otherwise not.
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, objectSize, print, save, asThis
Henrik Bengtsson
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.