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.
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"))
An AffymetrixCelSet.
Arguments passed to the constructor of
ProbeLevelTransform.
A character string for quickly specifying default
parameter settings.
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.
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".
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.
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.
A character string specifying what algorithm is used
to fit the crosstalk calibration.
Model fitting parameters.
A character string specifying how allele probe pairs
are identified.
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.
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.
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 signals should be
rescale together towards the target average (rescaleBy="all").
Methods:
process | - |
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, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
Henrik Bengtsson