Package: aroma.cn
Class TumorBoostNormalization
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="*", ...)
An AromaUnitFracBCnBinarySet
of
tumor samples.
An AromaUnitFracBCnBinarySet
of
match normal samples.
An AromaUnitGenotypeCallSet
of
genotypes for the normals.
A character
string specifying the type of
correction applied.
If 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 TumorBoost on SNPs that are homozygous in the matched normal.
If 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 FALSE
, the homozygous values are normalized according the
model. [NOT USED YET]
(Optional) Sets the tags for the output data sets.
Not used.
Methods:
getFullName | - | |
getInputDataSet | - | |
getName | - | |
getNormalDataSet | - | |
getNormalGenotypeCallSet | - | |
getOutputDataSet | - | |
getTags | - | |
nbrOfFiles | - | |
process | - | |
setTags | - |
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, Pierre Neuvial