TumorBoostNormalization: The TumorBoostNormalization class
In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

TumorBoostNormalization

R Documentation

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