Package: aroma.core
Class NonPairedPSCNData
data.frame
~~|
~~+--
RichDataFrame
~~~~~~~|
~~~~~~~+--
RawGenomicSignals
~~~~~~~~~~~~|
~~~~~~~~~~~~+--
AbstractCNData
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
AbstractPSCNData
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--
NonPairedPSCNData
Directly known subclasses:
public class NonPairedPSCNData
extends AbstractPSCNData
A NonPairedPSCNData object holds parent-specific copy number data.
Two NonPairedPSCNData objects for a matched tumor-normal pair can
be combined into a PairedPSCNData
object.
NonPairedPSCNData(chromosome=NULL, x=NULL, isSNP=NULL, mu=NULL, C=NULL, beta=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.
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 vector
s of length J.
Methods:
as | - | |
as.NonPairedPSCNData | - | |
as.PairedPSCNData | - | |
callNaiveGenotypes | - | |
callSegmentationOutliers | - | |
dropSegmentationOutliers | - | |
getSignalColumnNames | - | |
segmentByCBS | - |
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, split, split<-, stack, str, subset, summary, t, tail, transform, type.convert, unique, unstack, unwrap, within, wrap, writeDataFrame, xtfrm
Henrik Bengtsson