TumorBoostNormalization {aroma.cn}

The TumorBoostNormalization class

Description

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.

Usage

TumorBoostNormalization(dsT=NULL, dsN=NULL, gcN=NULL, flavor=c("v4", "v3", "v2", "v1"),
  preserveScale=TRUE, collapseHomozygous=FALSE, tags="*", ...)

Arguments

dsT

An AromaUnitFracBCnBinarySet of tumor samples.

dsN

An AromaUnitFracBCnBinarySet of match normal samples.

gcN

An AromaUnitGenotypeCallSet of genotypes for the normals.

flavor

A character string specifying the type of correction applied.

preserveScale

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.

collapseHomozygous

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]

tags

(Optional) Sets the tags for the output data sets.

...

Not used.

Fields and Methods

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

Author(s)

Henrik Bengtsson, Pierre Neuvial