AllelicCrosstalkCalibration: The AllelicCrosstalkCalibration class
Description
Package: aroma.affymetrix
Class AllelicCrosstalkCalibration
Object
~~|
~~+--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
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 i 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. B
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{
clearCache -
process Calibrates the data set.
}
Methods inherited from Transform:
getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles
Methods inherited from AromaTransform:
getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags
Methods inherited from Object:
asThis, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save