Package: aroma.core
Class AbstractPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
Directly known subclasses:
NonPairedPSCNData, PairedPSCNData
public class AbstractPSCNData
extends AbstractCNData
A AbstractPSCNData object holds parent-specific copy number data.
AbstractPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, ...)
(Optional) An integer
scalar (or a vector
of length J),
which can be used to specify which chromosome each locus belongs to
in case multiple chromosomes are segments.
This argument is also used for annotation purposes.
Optional numeric
vector
of J genomic locations.
If NULL
, index locations 1:J
are used.
An optional logical
vector
of length J specifying
whether each locus is a SNP or not (non-polymorphic loci).
An optional numeric
vector
of J genotype calls in
{0,1/2,1} for AA, AB, and BB, respectively,
and NA
for non-polymorphic loci.
Optional named locus-specific signal vector
s of length J.
Methods:
No methods defined.
Methods inherited from AbstractCNData:
findLargeGaps, getChipType, getLocusData, getPlatform, hasKnownPositions, orderAlongGenome, setChipType, setPlatform
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, 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
Henrik Bengtsson