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