FragmentLengthNormalization: The FragmentLengthNormalization class

Description

Package: aroma.affymetrix Class FragmentLengthNormalization

Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ChipEffectTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--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.

Usage

FragmentLengthNormalization(dataSet=NULL, ..., target=targetFunctions, subsetToFit="-XY", lengthRange=NULL, onMissing=c("median", "ignore"), shift=0, targetFunctions=NULL)

Arguments

dataSet

A SnpChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

target

(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.

subsetToFit

The units from which the normalization curve should be estimated. If NULL, all are considered.

lengthRange

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.

onMissing

Specifies how to normalize units for which the fragment lengths are unknown.

shift

An optional amount the data points should be shifted (translated).

targetFunctions

Deprecated.

Fields and Methods

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, objectSize, print, save, asThis

Requirements

This class requires a SNP information annotation file for the chip type to be normalized.

Details

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.