Object
~~|
~~+--TumorBoostNormalization
Directly known subclasses:
public static class TumorBoostNormalization
extends Object
TumorBoost is normalization method that normalizes the allele B fractions
of a tumor sample given the allele B fractions and genotype calls for
a matched normal.
The method is a single-sample (single-pair) method. It does not require
total copy number estimates.
The normalization is done such that the total copy number is unchanged
afterwards.TumorBoostNormalization(dsT=NULL, dsN=NULL, gcN=NULL, flavor=c("v4", "v3", "v2", "v1"), preserveScale=TRUE, collapseHomozygous=FALSE, tags="*", ...)AromaUnitFracBCnBinarySet of
tumor samples.AromaUnitFracBCnBinarySet of
match normal samples.AromaUnitGenotypeCallSet of
genotypes for the normals.character string specifying the type of
correction applied.TRUE, SNPs that are heterozygous in the
matched normal are corrected for signal compression using an estimate
of signal compression based on the amount of correction performed
by TRUE, SNPs that are homozygous in the
matched normal are also called homozygous in the tumor, that is,
it's allele B fraction is collapsed to either 0 or 1.
If getFullName -
getInputDataSet -
getName -
getNormalDataSet -
getNormalGenotypeCallSet -
getOutputDataSet -
getPath -
getRootPath -
getTags -
nbrOfFiles -
process -
setTags -
}
Methods inherited from Object:
asThis, getChecksum, $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save