LGG150                  LGG150 chromosomes 7-10
QDNAseq-package         Package QDNAseq
QDNAseqCopyNumbers      Container for QDNAseq read count data
QDNAseqReadCounts       Container for QDNAseq read count data
QDNAseqSignals          A parent class for containers of QDNAseq data
addPhenodata            Adds phenotype data from a file to a
                        QDNAseqReadCounts or a QDNAseqCopyNumbers
                        object
applyFilters            Adjusts the filtering on which bins are used
binReadCounts           Calculate binned read counts from a set of BAM
                        files
callBins                Call aberrations from segmented copy number
                        data
compareToReference      Divide binned read counts with those of
                        reference samples
correctBins             Correct binned read counts for GC content and
                        mappability
createBins              Builds bin annotation data for a particular bin
                        size
downloadBinAnnotations
                        Defunct functions in package 'QDNAseq'
estimateCorrection      Estimate correction to read counts for GC
                        content and mappability
exportBins              Exports to a file
frequencyPlot           Plot copy number aberration frequencies
getBinAnnotations       Gets bin annotation data for a particular bin
                        size
highlightFilters        Highlights data points in a plotted profile to
                        evaluate filtering
isobarPlot              Plot median read counts as a function of GC
                        content and mappability
makeCgh                 Constructs a 'cghRaw', 'cghSeg', or 'cghCall'
                        object
noisePlot               Plot noise as a function of sequence depth
normalizeBins           Normalizes binned read counts
normalizeSegmentedBins
                        Normalize segmented bins
plot                    Plot copy number profile
poolRuns                Pools binned read counts across samples
segmentBins             Segments normalized copy number data
smoothOutlierBins       Smooth outlier bins after normalization