Package: aroma.affymetrix
Class AdditiveCovariatesNormalization
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AdditiveCovariatesNormalization
Directly known subclasses:
GcContentNormalization2
public abstract static class AdditiveCovariatesNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for GC-content effects on copy-number chip-effect estimates.
AdditiveCovariatesNormalization(dataSet=NULL, ..., target=NULL, subsetToFit="-XY",
shift=0, onMissing=c("median", "ignore"))
A SnpChipEffectSet.
Additional arguments passed to the constructor of
ChipEffectTransform.
(Optional) A character string or a function
specifying what to normalize toward.
The units from which the normalization curve should
be estimated. If NULL, all are considered.
Specifies how to normalize units for which the GC contents are unknown.
An optional amount the data points should be shifted (translated).
Methods:
getCdf | - | |
process | - |
Methods inherited from ChipEffectTransform:
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
Henrik Bengtsson
For SNPs, the normalization function is estimated based on the total chip effects, i.e. the sum of the allele signals. The normalizing is done by rescale the chip effects on the intensity scale such that the mean of the total chip effects are the same across samples for any given GC content. For allele-specific estimates, both alleles are always rescaled by the same amount. Thus, when normalizing allele-specific chip effects, the total chip effects is change, but not the relative allele signal, e.g. the allele B frequency.