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%  AbstractCBS.R
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\name{AbstractCBS}
\docType{class}
\alias{AbstractCBS}


\title{The AbstractCBS class}

\description{
 Package:  PSCBS \cr
\bold{Class AbstractCBS}\cr

\code{list}\cr
\code{~~|}\cr
\code{~~+--}\emph{\code{AbstractCBS}}\cr

\bold{Directly known subclasses:}\cr
\emph{\link[PSCBS]{CBS}}, \emph{\link[PSCBS]{NonPairedPSCBS}}, \emph{\link[PSCBS]{PSCBS}}, \emph{\link[PSCBS]{PairedPSCBS}}\cr

public abstract static class \bold{AbstractCBS}\cr
extends list\cr



 All CBS-style segmentation results extend this class, e.g.
 \code{\link{CBS}} and \code{\link{PairedPSCBS}}.
}

\usage{
AbstractCBS(fit=list(), sampleName=fit$sampleName, ...)
}

\arguments{
  \item{fit}{A \code{\link[base]{list}} structure containing the segmentation results.}
  \item{sampleName}{A \code{\link[base]{character}} string.}
  \item{...}{Not used.}
}

\section{Fields and Methods}{
 \bold{Methods:}\cr
\tabular{rll}{
 \tab \code{adjustPloidyScale} \tab  -\cr
 \tab \code{\link[PSCBS:append.AbstractCBS]{append}} \tab Appends one segmentation result to another.\cr
 \tab \code{extractCNs} \tab  -\cr
 \tab \code{getChangePoints} \tab  -\cr
 \tab \code{\link[PSCBS:getChromosomes.AbstractCBS]{getChromosomes}} \tab Gets the set of chromosomes.\cr
 \tab \code{\link[PSCBS:getLocusData.AbstractCBS]{getLocusData}} \tab Gets the locus-level data.\cr
 \tab \code{getSegmentSizes} \tab  -\cr
 \tab \code{\link[PSCBS:getSegments.AbstractCBS]{getSegments}} \tab Gets the segments.\cr
 \tab \code{\link[PSCBS:load.AbstractCBS]{load}} \tab Loads an AbstractCBS object from file.\cr
 \tab \code{\link[PSCBS:mergeThreeSegments.AbstractCBS]{mergeThreeSegments}} \tab Merge a segment and its two flanking segments.\cr
 \tab \code{\link[PSCBS:nbrOfChangePoints.AbstractCBS]{nbrOfChangePoints}} \tab Gets the number of change points.\cr
 \tab \code{\link[PSCBS:nbrOfChromosomes.AbstractCBS]{nbrOfChromosomes}} \tab Gets the number of chromosomes.\cr
 \tab \code{\link[PSCBS:nbrOfLoci.AbstractCBS]{nbrOfLoci}} \tab Gets the number of loci.\cr
 \tab \code{\link[PSCBS:nbrOfSegments.AbstractCBS]{nbrOfSegments}} \tab Gets the number of segments.\cr
 \tab \code{\link[PSCBS:normalizeTotalCNs.AbstractCBS]{normalizeTotalCNs}} \tab Normalizes copy numbers such that the whole-genome average total copy number is two.\cr
 \tab \code{\link[PSCBS:ploidy.AbstractCBS]{ploidy}} \tab Gets and sets ploidy.\cr
 \tab \code{ploidy<-} \tab  -\cr
 \tab \code{\link[PSCBS:plotTracks.AbstractCBS]{plotTracks}} \tab Plots the segmentation result along the genome.\cr
 \tab \code{sampleCNs} \tab  -\cr
 \tab \code{\link[PSCBS:save.AbstractCBS]{save}} \tab Saves an AbstractCBS object to file.\cr
 \tab \code{writeWIG} \tab  -\cr
}


 \bold{Methods inherited from list}:\cr
Ops,nonStructure,vector-method, Ops,structure,vector-method, Ops,vector,nonStructure-method, Ops,vector,structure-method, all.equal, as.data.frame, attachLocally, averageQuantile, callHooks, coerce,ANY,list-method, coerce,Matrix,vector-method, coerce,abIndex,vector-method, coerce,dgCMatrix,vector-method, coerce,dsCMatrix,vector-method, coerce,list,indMatrix-method, coerce,sparseVector,vector-method, contents, ggplot_add, latex, normalizeAverage, normalizeDifferencesToAverage, normalizeQuantileRank, normalizeQuantileSpline, plotDensity, relist, scale_type, type.convert, within, wrap


}

\author{Henrik Bengtsson}


\keyword{classes}
\keyword{internal}
