# Quantitative DNA Sequencing for Chromosomal Aberrations

## Documentation for package ‘QDNAseq’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
calculateBlacklistByRegions | 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