PairedPscbsModel | R Documentation |
Package: aroma.cn
Class PairedPscbsModel
Object
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ParametersInterface
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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.
PairedPscbsModel(dsT=NULL, dsN=NULL, tags="*", ..., dropTcnOutliers=TRUE, gapMinLength=1e+06, seed=NULL)
dsT, dsN |
The tumor and the normal
|
tags |
Tags added to the output data sets. |
... |
(Optional) Additional arguments passed to
|
dropTcnOutliers |
If |
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 + |
seed |
An optional |
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:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
[1] ...
...
## Not run: dataSet <- "GSE12702" tags <- "ASCRMAv2" chipType <- "Mapping250K_Nsp" ds <- AromaUnitPscnBinarySet$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)
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