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

PairedPscbsModel

R Documentation

The PairedPscbsModel class

Description

Package: aroma.cn
Class PairedPscbsModel

Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--PairedPscbsModel

Directly known subclasses:

public static class PairedPscbsModel
extends ParametersInterface

This class represents the Paired PSCBS method [1], which segments matched tumor-normal parental copy-number data into piecewise constant segments.

Usage

PairedPscbsModel(dsT=NULL, dsN=NULL, tags="*", ..., dropTcnOutliers=TRUE,
  gapMinLength=1e+06, seed=NULL)

Arguments

`dsT, dsN`	The tumor and the normal `AromaUnitPscnBinarySet`.
`tags`	Tags added to the output data sets.
`...`	(Optional) Additional arguments passed to `segmentByPairedPSCBS`.
`dropTcnOutliers`	If `TRUE`, then TCN outliers are dropped using `dropSegmentationOutliers`.
`gapMinLength`	Genomic regions with no data points that are of this length and greater are considered to be "gaps" and are ignored in the segmentation. If +`Inf`, no gaps are identified.
`seed`	An optional `integer` specifying the random seed to be used in the segmentation. Seed needs to be set for exact numerical reproducibility.

Fields and Methods

Methods:

	`fit`	-
	`getChipType`	-
	`getChromosomes`	-
	`getDataSets`	-
	`getFullName`	-
	`getName`	-
	`getNormalDataSet`	-
	`getOutputDataSet`	-
	`getTags`	-
	`getTumorDataSet`	-
	`indexOf`	-
	`nbrOfFiles`	-
	`setTags`	-

Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString

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

References

[1] ...

Examples

## Not run: 
  dataSet <- "GSE12702"
tags <- "ASCRMAv2"
chipType <- "Mapping250K_Nsp"
ds <- AromaUnitPscnBinarySet$byName(dataSet, tags=tags, chipType=chipType)
print(ds)

# Extract tumors and normals
idxs <- seq(from=1, to=nbrOfFiles(ds), by=2)
dsT <- extract(ds, idxs);
idxs <- seq(from=2, to=nbrOfFiles(ds), by=2)
dsN <- extract(ds, idxs);

# Setup Paired PSCBS model
seg <- PairedPscbsModel(dsT=dsT, dsN=dsN)
print(seg)

# Segment all tumor-normal pairs
fit(seg, verbose=-10)


## End(Not run)

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.