Package: aroma.core
Class PairedPSCNData
data.frame
~~|
~~+--RichDataFrame
~~~~~~~|
~~~~~~~+--RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--PairedPSCNData
Directly known subclasses:
public class PairedPSCNData
extends AbstractPSCNData
A PairedPSCNData object holds paired tumor-normal parent-specific copy number data.
PairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, muN=NULL, CT=NULL, betaT=NULL,
CN=NULL, betaN=NULL, ...)
A numeric vector of J tumor total copy number (TCN)
ratios in [0,+Inf) (due to noise, small negative values are
also allowed). The TCN ratios are typically scaled such that
copy-neutral diploid loci have a mean of two.
A numeric vector of J tumor allele B fractions (BAFs)
in [0,1] (due to noise, values may be slightly outside as well)
or NA for non-polymorphic loci.
A numeric vector of J matched normal BAFs in [0,1]
(due to noise, values may be slightly outside as well) or NA
for 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.
If not given, they are estimated from the normal BAFs using
callNaiveGenotypes as described in [2].
An optional logical vector of length J specifying
whether each locus is a SNP or not (non-polymorphic loci).
(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.
Optional named locus-specific signal vectors of length J.
Methods:
as | - | |
as.PairedPSCNData | - | |
callNaiveGenotypes | - | |
callSegmentationOutliers | - | |
dropSegmentationOutliers | - | |
getSignalColumnNames | - | |
getTCNs | - | |
getTotalCopyNumbers | - | |
normalizeTumorBoost | - | |
plotTracks | - | |
segmentByCBS | - | |
segmentByPairedPSCBS | - |
Methods inherited from AbstractPSCNData:
callSNPs, getSNPFields
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, plotDensity, print, prompt, rbind, row.names, row.names<-, rowsum, segmentByCBS, segmentByPairedPSCBS, show,oldClass-method, slotsFromS3,data.frame-method, sort_by, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson