Man pages for QDNAseq
Quantitative DNA Sequencing for Chromosomal Aberrations

addPhenodataAdds phenotype data from a file to a QDNAseqReadCounts or a...
applyFiltersAdjusts the filtering on which bins are used
binReadCountsCalculate binned read counts from a set of BAM files
callBinsCall aberrations from segmented copy number data
compareToReferenceDivide binned read counts with those of reference samples
correctBinsCorrect binned read counts for GC content and mappability
createBinsBuilds bin annotation data for a particular bin size
estimateCorrectionEstimate correction to read counts for GC content and...
exportBinsExports to a file
frequencyPlotPlot copy number aberration frequencies
getBinAnnotationsGets bin annotation data for a particular bin size
highlightFiltersHighlights data points in a plotted profile to evaluate...
isobarPlotPlot median read counts as a function of GC content and...
LGG150LGG150 chromosomes 7-10
makeCghConstructs a 'cghRaw', 'cghSeg', or 'cghCall' object
noisePlotPlot noise as a function of sequence depth
normalizeBinsNormalizes binned read counts
normalizeSegmentedBinsNormalize segmented bins
plotPlot copy number profile
poolRunsPools binned read counts across samples
QDNAseqCopyNumbersContainer for QDNAseq read count data
QDNAseq-defunctDefunct functions in package 'QDNAseq'
QDNAseq-packagePackage QDNAseq
QDNAseqReadCountsContainer for QDNAseq read count data
QDNAseqSignalsA parent class for containers of QDNAseq data
segmentBinsSegments normalized copy number data
smoothOutlierBinsSmooth outlier bins after normalization
QDNAseq documentation built on Nov. 8, 2020, 6:57 p.m.