PairedPscbsModel: The PairedPscbsModel class

Description Usage Arguments Fields and Methods References See Also Examples

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

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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, objectSize, print, save, asThis

References

[1] ...

See Also

...

Examples

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## 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)

aroma.cn documentation built on May 29, 2017, 7:56 p.m.