Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
|Author||Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut]|
|Date of publication||None|
|Maintainer||Daoud Sie <email@example.com>|
addPhenodata: Adds phenotype data from a file to a QDNAseqReadCounts or a...
applyFilters: Adjusts the filtering on which bins are used
binReadCounts: Calculate binned read counts from a set of BAM files
callBins: Call aberrations from segmented copy number data
compareToReference: Divide binned read counts with those of reference samples
correctBins: Correct binned read counts for GC content and mappability
createBins: Builds bin annotation data for a particular bin size
estimateCorrection: Estimate correction to read counts for GC content and...
exportBins: Exports to a file
frequencyPlot: 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...
isobarPlot: Plot median read counts as a function of GC content and...
LGG150: LGG150 chromosomes 7-10
makeCgh: Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object
noisePlot: Plot noise as a function of sequence depth
normalizeBins: Normalizes binned read counts
normalizeSegmentedBins: Normalize segmented bins
plot: Plot copy number profile
poolRuns: Pools binned read counts across samples
QDNAseqCopyNumbers: Container for QDNAseq read count data
QDNAseq-defunct: Defunct functions in package 'QDNAseq'
QDNAseq-package: Package QDNAseq
QDNAseqReadCounts: Container for QDNAseq read count data
QDNAseqSignals: A parent class for containers of QDNAseq data
segmentBins: Segments normalized copy number data
smoothOutlierBins: Smooth outlier bins after normalization