SegmentedAlleleBFractions {aroma.core}

The SegmentedAlleleBFractions class

Description

Package: aroma.core
Class SegmentedAlleleBFractions

data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--RawAlleleBFractions
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--SegmentedGenomicSignalsInterface
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--SegmentedAlleleBFractions

Directly known subclasses:

public class SegmentedAlleleBFractions
extends SegmentedGenomicSignalsInterface

Usage

SegmentedAlleleBFractions(..., states=NULL)

Arguments

...

Arguments passed to RawAlleleBFractions.

states

A function returning the copy-number states given a vector of locus positions.

Fields and Methods

Methods:
No methods defined.

Methods inherited from SegmentedGenomicSignalsInterface:
as.data.frame, binnedSmoothingByState, extractSubsetByState, findChangePointsByState, getStateColorMap, getStateColors, getStates, getUniqueStates, getVirtualField, getVirtualLocusFields, kernelSmoothingByState, plot, points, setStateColorMap, setStates

Methods inherited from RawAlleleBFractions:
extractRawMirroredAlleleBFractions, plot

Methods inherited from RawGenomicSignals:
*, +, -, addBy, append, applyBinaryOperator, as.character, as.data.frame, assertOneChromosome, binnedSmoothing, binnedSmoothingByField, clearCache, clone, divideBy, drawDensity, estimateStandardDeviation, extractChromosome, extractChromosomes, extractDataForSegmentation, extractRegion, extractRegions, extractSubset, gaussianSmoothing, getBasicField, getCXY, getChromosome, getChromosomes, getDefaultLocusFields, getLocusFields, getPositions, getSigma, getSignalColumnName, getSignalColumnNames, getSignals, getWeights, getXScale, getXY, getYScale, hasWeights, kernelSmoothing, lines, multiplyBy, nbrOfChromosomes, nbrOfLoci, plot, points, print, segmentByCBS, segmentByGLAD, segmentByHaarSeg, segmentByMPCBS, setBasicField, setSigma, setSignals, setWeights, setXScale, setYScale, signalRange, sort, subtractBy, xMax, xMin, xRange, xSeq, yMax, yMin, yRange

Methods inherited from RichDataFrame:
$, $<-, [, [[, [[<-, as.data.frame, as.list, dim, dropVirtualColumn, getColumnNames, getColumnNamesTranslator, getFullName, getName, getTags, getVirtualColumn, getVirtualColumnFunction, getVirtualColumnNames, hasColumn, hasColumns, hasVirtualColumn, hasVirtualColumns, length, names, newInstance, print, rbind, setAttributes, setColumnNamesMap, setColumnNamesTranslator, setName, setTags, setVirtualColumn, subset, translateColumnNames

Methods inherited from data.frame:
$<-,data.frame-method, $<-, Math, Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, Ops, Summary, [, [<-,data.frame-method, [<-, [[, [[<-,data.frame-method, [[<-, aggregate, anyDuplicated, anyNA, as.NonPairedPSCNData, as.PairedPSCNData, as.data.frame, as.list, as.matrix, as.vector, attachLocally, by, callSegmentationOutliers, cbind, coerce,ANY,list-method, coerce,oldClass,S3-method, dim, dimnames, dimnames<-, dropSegmentationOutliers, droplevels, duplicated, edit, findLargeGaps, format, formula, head, initialize,oldClass-method, is.na, merge, na.exclude, na.omit, plot, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm

Author(s)

Henrik Bengtsson