AllelicCrosstalkCalibration: The AllelicCrosstalkCalibration class

Description

Package: aroma.affymetrix Class AllelicCrosstalkCalibration Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ProbeLevelTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AllelicCrosstalkCalibration Directly known subclasses: public static class AllelicCrosstalkCalibration extends ProbeLevelTransform This class represents a calibration function that transforms the probe-level signals such that the signals from the two alleles are orthogonal. The method fits and calibrates PM signals only. MM signals will not affect the model fitting and are unaffected.

Usage

AllelicCrosstalkCalibration(dataSet=NULL, ..., model=c("asis", "auto", "CRMA", "CRMAv2"),
  rescaleBy=c("auto", "groups", "all", "none"), targetAvg=c(2200, 2200),
  subsetToAvg="-XY", mergeShifts=TRUE, B=1, flavor=c("sfit", "expectile"),
  alpha=c(0.1, 0.075, 0.05, 0.03, 0.01), q=2, Q=98, lambda=2,
  pairBy=c("CDF", "sequence"))

Arguments

dataSet

An AffymetrixCelSet.

...

Arguments passed to the constructor of ProbeLevelTransform.

model

A character string for quickly specifying default parameter settings.

rescaleBy

A character string specifying what sets of cells should be rescaled towards a target average, if any. Default is to rescale all cells together. If "none", no rescaling is done

targetAvg

The signal(s) that either the average of the sum (if one target value) or the average of each of the alleles (if two target values) should have after calibration. Only used if rescaleBy != "none".

subsetToAvg

The indices of the cells (taken as the intersect of existing indices) used to calculate average in order to rescale to the target average. If NULL, all probes are considered.

mergeShifts

If TRUE, the shift of the probe sequence relative to the SNP position is ignored, otherwise not.

An integer specifying by how many nucleotides the allelic groups should be stratified by. If zero, all SNPs are put in one group.

flavor

A character string specifying what algorithm is used to fit the crosstalk calibration.

alpha, q, Q, lambda

Model fitting parameters.

pairBy

A character string specifying how allele probe pairs are identified.

What probe signals are updated?

Calibration for crosstalk between allele signals applies by definition only SNP units. Furthermore, it is only SNP units with two or four unit groups that are calibrated. For instance, in at least on custom SNP CDFs we know of, there is a small number of SNP units that have six groups. Currently these units are not calibrated (at all). It is only PM probes that will be calibrated. Note that, non-calibrated signals will be saved in the output files.

What probe signals are used to fit model?

All PM probe pairs are used to fit the crosstalk model. In the second step where signals are rescaled to a target average, it is possible to specify the set of cells that should be included when estimating the target average.

Important about rescaling towards target average

Rescaling each allele-pair group (e.g. AC, AG, AT, CG, CT, GC) towards a target average (rescaleBy="groups") must not be used for multi-enzyme chip types, e.g. GenomeWideSNP_6. If still done, due to confounded effects of non-perfect enzyme mixtures etc, there will be a significant bias between raw CNs for SNPs and CN probes. Instead, for such chip types all probe signales should be rescale together towards the target average (rescaleBy="all").

Fields and Methods

Methods: rll{ process Calibrates the data set. }

Methods inherited from ProbeLevelTransform: 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, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis