QDNAseq: Quantitative DNA sequencing for chromosomal aberrations

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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 <d.sie@vumc.nl>
License
GPL
Version
1.10.0
URLs

View on Bioconductor

Man pages

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

Files in this package

QDNAseq/DESCRIPTION
QDNAseq/NAMESPACE
QDNAseq/NEWS
QDNAseq/R
QDNAseq/R/998.LGG150.R
QDNAseq/R/999.package.R
QDNAseq/R/AllClasses.R
QDNAseq/R/AllGenerics.R
QDNAseq/R/QDNAseqCopyNumbers-accessors.R
QDNAseq/R/QDNAseqReadCounts-accessors.R
QDNAseq/R/QDNAseqSignals-accessors.R
QDNAseq/R/addPhenodata.R
QDNAseq/R/applyFilters.R
QDNAseq/R/binReadCounts.R
QDNAseq/R/callBins.R
QDNAseq/R/compareToReference.R
QDNAseq/R/correctBins.R
QDNAseq/R/createBinAnnotations.R
QDNAseq/R/estimateCorrection.R
QDNAseq/R/exportBins.R
QDNAseq/R/getBinAnnotations.R
QDNAseq/R/highlightFilters.R
QDNAseq/R/logTransform.R
QDNAseq/R/makeCgh.R
QDNAseq/R/normalizeBins.R
QDNAseq/R/normalizeSegmentedBins.R
QDNAseq/R/plot-methods.R
QDNAseq/R/poolRuns.R
QDNAseq/R/sdDiffTrim.R
QDNAseq/R/segmentBins.R
QDNAseq/R/smoothOutlierBins.R
QDNAseq/R/utils.R
QDNAseq/R/vmsg.R
QDNAseq/build
QDNAseq/build/vignette.rds
QDNAseq/data
QDNAseq/data/LGG150.rda
QDNAseq/inst
QDNAseq/inst/CITATION
QDNAseq/inst/doc
QDNAseq/inst/doc/QDNAseq.R
QDNAseq/inst/doc/QDNAseq.Rnw
QDNAseq/inst/doc/QDNAseq.pdf
QDNAseq/man
QDNAseq/man/LGG150.Rd
QDNAseq/man/QDNAseq-defunct.Rd
QDNAseq/man/QDNAseq-package.Rd
QDNAseq/man/QDNAseqCopyNumbers.Rd
QDNAseq/man/QDNAseqReadCounts.Rd
QDNAseq/man/QDNAseqSignals.Rd
QDNAseq/man/addPhenodata.Rd
QDNAseq/man/applyFilters.Rd
QDNAseq/man/binReadCounts.Rd
QDNAseq/man/callBins.Rd
QDNAseq/man/compareToReference.Rd
QDNAseq/man/correctBins.Rd
QDNAseq/man/createBins.Rd
QDNAseq/man/estimateCorrection.Rd
QDNAseq/man/exportBins.Rd
QDNAseq/man/frequencyPlot.Rd
QDNAseq/man/getBinAnnotations.Rd
QDNAseq/man/highlightFilters.Rd
QDNAseq/man/isobarPlot.Rd
QDNAseq/man/makeCgh.Rd
QDNAseq/man/noisePlot.Rd
QDNAseq/man/normalizeBins.Rd
QDNAseq/man/normalizeSegmentedBins.Rd
QDNAseq/man/plot.Rd
QDNAseq/man/poolRuns.Rd
QDNAseq/man/segmentBins.Rd
QDNAseq/man/smoothOutlierBins.Rd
QDNAseq/tests
QDNAseq/tests/QDNAseq,reproducibility.R
QDNAseq/tests/QDNAseq.R
QDNAseq/vignettes
QDNAseq/vignettes/QDNAseq.Rnw