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 |