QDNAseq-package	QDNAseq-package
addPhenodata	addPhenodata
applyFilters	applyFilters
applyFilters,QDNAseqReadCounts-method	applyFilters
binReadCounts	binReadCounts
bpend,QDNAseqSignals-method	QDNAseqSignals
bpstart,QDNAseqSignals-method	QDNAseqSignals
calculateBlacklist	createBins
calculateMappability	createBins
callBins	callBins
callBins,QDNAseqCopyNumbers-method	callBins
chromosomes,QDNAseqSignals-method	QDNAseqSignals
compareToReference	compareToReference
compareToReference,QDNAseqCopyNumbers,numeric-method	compareToReference
correctBins	correctBins
correctBins,QDNAseqReadCounts-method	correctBins
createBins	createBins
downloadBinAnnotations	QDNAseq-defunct
estimateCorrection	estimateCorrection
estimateCorrection,QDNAseqReadCounts-method	estimateCorrection
exportBins	exportBins
exportBins,QDNAseqSignals-method	exportBins
frequencyPlot	frequencyPlot
frequencyPlot,QDNAseqCopyNumbers,missing-method	frequencyPlot
getBinAnnotations	getBinAnnotations
highlightFilters	highlightFilters
highlightFilters,QDNAseqSignals-method	highlightFilters
isobarPlot	isobarPlot
isobarPlot,QDNAseqReadCounts,missing-method	isobarPlot
iterateResiduals	createBins
LGG150	LGG150
makeCgh	makeCgh
makeCgh,QDNAseqCopyNumbers-method	makeCgh
noisePlot	noisePlot
noisePlot,QDNAseqReadCounts,missing-method	noisePlot
normalizeBins	normalizeBins
normalizeBins,QDNAseqCopyNumbers-method	normalizeBins
normalizeSegmentedBins	normalizeSegmentedBins
normalizeSegmentedBins,QDNAseqCopyNumbers-method	normalizeSegmentedBins
plot	plot
plot,QDNAseqSignals,missing-method	plot
poolRuns	poolRuns
poolRuns,QDNAseqSignals,character-method	poolRuns
QDNAseq	QDNAseq-package
QDNAseqCopyNumbers	QDNAseqCopyNumbers
QDNAseqCopyNumbers-class	QDNAseqCopyNumbers
QDNAseqReadCounts	QDNAseqReadCounts
QDNAseqReadCounts-class	QDNAseqReadCounts
QDNAseqSignals	QDNAseqSignals
QDNAseqSignals-class	QDNAseqSignals
segmentBins	segmentBins
segmentBins,QDNAseqCopyNumbers-method	segmentBins
smoothOutlierBins	smoothOutlierBins
smoothOutlierBins,QDNAseqCopyNumbers-method	smoothOutlierBins
