The SNPsNormalization class

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Description

Package: NSA
Class SNPsNormalization

Object
~~|
~~+--SNPsNormalization

Directly known subclasses:

public static class SNPsNormalization
extends Object

This class represents the SNPs normalization method [1], which corrects for SNP effects in allele-specific copy-number estimates (ASCNs).

Usage

1

Arguments

data

A named list with data set named "total" and "fracB" where the former should be of class AromaUnitTotalCnBinarySet and the latter of class AromaUnitFracBCnBinarySet. The two data sets must be for the same chip type, have the same number of samples and the same sample names.

tags

Tags added to the output data sets.

...

Not used.

Details

...

Fields and Methods

Methods:

findUnitsTodo -
getDataSets -
getFullName -
getName -
getOutputDataSets -
getPath -
getRootPath -
getTags -
nbrOfFiles -
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

References

[1] ...

See Also

Low-level versions of the SNPs normalization method is available via snpsNByTotalAndFracB.matrix() methods.