AbstractCBS
AppVeyor
BAF
BAFs
BMC
Bioinformatics
Biostatistics
CGH
CMD
CN
Chr
CxK
DHs
DNAcopy
Fridlyand
Homozygosity
JxL
LOH
Lucito
NTCN
NonPairedPSCBS
PSCN
PairedPSCBS
Pre
ROH
RSP
Reproducibility
SxK
TCN
TCNs
TumorBoost
UCSF
Venkatraman
Wigler
abIndex
adjustPloidyScale
al
allelic
amplificationCall
attachLocally
averageQuantile
callHooks
changepoints
clearCalls
dgCMatrix
drawChangePoints
drawKnownSegments
dropChangePoint
dropChangePoints
dropRegion
dropRegions
dsCMatrix
et
extractCNs
extractChromosome
extractChromosomes
extractRegions
extractSegments
extractWIG
gainCall
genomewide
germline
getChangePoints
getChromosomeOffsets
getChromosomeRanges
getChromosomes
getLocusData
getLocusSignalNames
getMeanEstimators
getSampleName
getSegmentSizes
getSegmentTrackPrefixes
getSegments
ggplot
hclust
heterozygosity
heterozygous
homozygosity
homozygous
indMatrix
isLocallyPhased
isSegmentSplitter
lossCall
macOS
mergeThreeSegments
mergeTwoSegments
minDensity
nbrOfChangePoints
nbrOfChromosomes
nbrOfLoci
nbrOfSegments
negOutlierCall
nonStructure
normalizeAverage
normalizeDifferencesToAverage
normalizeQuantileRank
normalizeQuantileSpline
normalizeTotalCNs
normals
phenotypes
ploidy
plotDensity
plotTracks
posOutlierCall
pre
pruneByDP
pruneByHClust
renameChromosomes
rescaling
resegment
resetSegments
sampleCNs
sampleName
segements
segmentions
seperately
seqOfSegmentsByDP
setLocusData
setMeanEstimators
setPloidy
setSampleName
setSegments
shiftTCN
sparseVector
splitters
subclasses
th
tileChromosomes
updateMeans
writeSegments
writeWIG
abCall
ABO
AbstractPSCBS
addCalls
addtolength
adjustFor
alltt
alphaAB
alphaDH
alphaHighAI
alphaTCN
anyMissing
appendVarArgs
applyByRegion
args
arrowsC
arrowsDeltaC
asMissing
aspectRatio
AtNonAB
attr
avgDH
avgTCN
Bengtsson
BengtssonH
betaN
betaT
betaTN
bibliographystyle
BioC
biocViews
bionomial
Blim
bootstrapDHByRegion
bootstrapSegmentsAndChangepoints
bootstrapTCNandDHByRegion
bottomfraction
bottomnumber
bs
bst
ByC
calcStatsForCopyNeutralABs
callAB
callABandHighAI
callABandLowC
callAllelicBalance
callAllelicBalanceByDH
callAmplifications
callArms
callCopyNeutral
callCopyNeutralByTCNofAB
callExtremeAllelicImbalance
callExtremeAllelicImbalanceByDH
callGainNeutralLoss
callGainsAndLosses
callGLAO
callGNL
callLoci
callLOH
callLowC
callNaiveGenotypes
callNaiveHeterzygotes
callNnn
callNTCN
callROH
callSegmentationOutliers
callSegments
camelCase
centromere
centromeres
cex
chr
ciRange
citep
citet
className
clearBootstrapSummaries
clearpage
Clim
CMRG
cn
CNA
columnNamesFlavor
cran
csN
datapoint
deltaAB
deltaCN
deltaLOH
DeltaLOH
deltaROH
dev
devEval
devOptions
dh
dhNbrOfLoci
dhSegRows
dmad
documentclass
downsampled
drawChromosomes
drawConfidenceBands
drawLevels
dropGaps
dropMissingCT
dropSegmentationOutliers
dt
emph
encodeCalls
ensuremath
escapeRspVerbatim
estimateDeltaAB
estimateDeltaCN
estimateDeltaLOH
estimateDeltaLOHByMinC
estimateHighDHQuantileAtAB
estimateKappa
estimateKappaByC
estimateStandardDeviation
estimateTauAB
estimateTauABBySmallDH
estimateTauLOH
estimateTauLOHByMinC
etal
evensidemargin
exampleData
exData
extractByChromosome
extractByChromosomes
extractByRegions
extractMinorMajorCNs
extractSegment
extractSegmentDataByLocus
extractTCNAndDHs
extractTotalCNs
exts
figTracks
figTracksPruned
findheterozygous
findLargeGaps
findNeutralCopyNumberState
findPeaksAndValleys
fitP
fixLocations
floatpagefraction
footnotesize
ForNonAB
fullname
gapsToSegments
GC
genomeData
GenomeWideSNP
getbdry
getBootstrapLocusSets
getCallStatistics
getCallStatisticsByArms
getSmoothLocusData
graphicspath
graphicx
hclustCNs
heterozygotes
heterozyous
hidelinks
highlightArmCalls
Hmisc
homozygote
homozygotes
hrmode
htp
https
hyperref
hypersetup
Ilari
Illumina
includegraphics
installDNAcopy
jj
joinSegments
Junsong
Kirill
knownCPs
knownSegments
listenv
loadMethod
loadObject
lociNotPartOfSegment
loh
lohCall
magnitutes
Makefile
maketitle
maploc
matchings
matrixStats
maxC
meanCol
memoization
methodsS
minLength
minSize
Minya
multipage
multisession
muN
MySample
na
NaN
natbib
nbrOfUnits
neglectable
newcommand
newenvironment
NextMethod
nnn
nnstedt
normalizeTumorBoost
nperm
nrow
nucleotides
num
oddsidemargin
OlshenA
oma
onAttach
oo
PairedPSCNSegments
parskip
pdfauthor
pdfborder
pdfkeywords
pdfproducer
pdfsubject
pdftitle
plotTrack
plotTracksManyChromosomes
png
postsegmentTCN
preserveOrder
preserveScale
priorly
probs
pruneBySdUndo
psCBS
PSCBS
psSegment
psSegmentPaired
renewcommand
resegmentation
resizebox
rfile
Rinstignore
Ritu
rowAlls
rsp
rspTags
rspVerbatim
Rueda
sanityChecks
saveObject
Scheinin
sdundo
secBackground
secData
secGaps
secTCNOutliers
segJJ
segmentations
segmentByCBS
segmentByNonPairedPSCBS
segmentByPairedPSCBS
segs
sessionInfo
setcounter
setMethodS
setOption
signalType
Similarily
splitter
startupMessage
stopifnot
str
strOptions
studyName
subsetBySegments
subsubsection
Sys
tableofcontents
Talevich
tauA
tauAB
tauB
tauTCN
tbn
tcn
tcnNbrOfHets
tcnnbrOfLoci
tcnNbrOfLoci
tcnNbrOfSNPs
tcnNbrOr
tcnSegRows
testROH
tex
textbf
textfraction
textheight
textnormal
textsl
texttt
textwidth
thetaN
thetaT
tiledChromosomes
tmp
toLatex
topfraction
topmargin
toPNG
Tsukanov
TumorBoosted
TumorBoostNormalization
typeOfWeights
UC
ucsf
undoDH
undoTCN
unlist
unTumorBoost
updateBoundaries
updateMeansC
updateMeansTogether
useAlphaChannel
usepackage
VenkatramanOlshen
VignetteAuthor
VignetteBuilder
VignetteEngine
VignetteIndexEntry
VignetteKeyword
vspace
VUMC
WEHI
weightedMedian
weightedQuantile
whichVector
withCapture
writeLocusData
xBEEF
xcolor
xlim
xorCalls
xspace
Zhao
L'Ecuyer
NaN's
psCNA
segmentByNnn
segRows
