Quantitative DNA sequencing for chromosomal aberrations


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Documentation for package ‘QDNAseq’ version 1.6.1

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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