Package: aroma.affymetrix
Class FragmentLengthNormalization
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
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~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ChipEffectTransform
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~~~~~~~~~~~~~~~~~~~~~~+--FragmentLengthNormalization
Directly known subclasses:
public static class FragmentLengthNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for PCR fragment length effects on copy-number chip-effect estimates.
FragmentLengthNormalization(dataSet=NULL, ..., target=targetFunctions, subsetToFit="-XY",
lengthRange=NULL, onMissing=c("median", "ignore"), shift=0, targetFunctions=NULL)
A SnpChipEffectSet.
Additional arguments passed to the constructor of
ChipEffectTransform.
(Optional) A character string or a list of functions
specifying what to normalize toward.
For each enzyme there is one target function to which all arrays
should be normalized to.
The units from which the normalization curve should
be estimated. If NULL, all are considered.
If given, a numeric vector of length 2 specifying
the range of fragment lengths considered. All fragments with lengths
outside this range are treated as if they were missing.
Specifies how to normalize units for which the fragment lengths are unknown.
An optional amount the data points should be shifted (translated).
Deprecated.
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
This class requires a SNP information annotation file for the chip type to be normalized.
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 fragment length. 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.