QDNAseq: Quantitative DNA sequencing for chromosomal aberrations

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.

AuthorIlari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut]
Date of publicationNone
MaintainerDaoud Sie <d.sie@vumc.nl>
LicenseGPL
Version1.10.0
https://github.com/ccagc/QDNAseq

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

Functions

addPhenodata Man page
applyFilters Man page
applyFilters,QDNAseqReadCounts-method Man page
binReadCounts Man page
bpend,QDNAseqSignals-method Man page
bpstart,QDNAseqSignals-method Man page
calculateBlacklist Man page
calculateMappability Man page
callBins Man page
callBins,QDNAseqCopyNumbers-method Man page
chromosomes,QDNAseqSignals-method Man page
compareToReference Man page
compareToReference,QDNAseqCopyNumbers,numeric-method Man page
correctBins Man page
correctBins,QDNAseqReadCounts-method Man page
createBins Man page
downloadBinAnnotations Man page
estimateCorrection Man page
estimateCorrection,QDNAseqReadCounts-method Man page
exportBins Man page
exportBins,QDNAseqSignals-method Man page
frequencyPlot Man page
frequencyPlot,QDNAseqCopyNumbers,missing-method Man page
getBinAnnotations Man page
highlightFilters Man page
highlightFilters,QDNAseqSignals-method Man page
isobarPlot Man page
isobarPlot,QDNAseqReadCounts,missing-method Man page
iterateResiduals Man page
LGG150 Man page
makeCgh Man page
makeCgh,QDNAseqCopyNumbers-method Man page
noisePlot Man page
noisePlot,QDNAseqReadCounts,missing-method Man page
normalizeBins Man page
normalizeBins,QDNAseqCopyNumbers-method Man page
normalizeSegmentedBins Man page
normalizeSegmentedBins,QDNAseqCopyNumbers-method Man page
plot Man page
plot,QDNAseqSignals,missing-method Man page
poolRuns Man page
poolRuns,QDNAseqSignals,character-method Man page
QDNAseq Man page
QDNAseqCopyNumbers Man page
QDNAseqCopyNumbers-class Man page
QDNAseq-package Man page
QDNAseqReadCounts Man page
QDNAseqReadCounts-class Man page
QDNAseqSignals Man page
QDNAseqSignals-class Man page
segmentBins Man page
segmentBins,QDNAseqCopyNumbers-method Man page
smoothOutlierBins Man page
smoothOutlierBins,QDNAseqCopyNumbers-method Man page

Files

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

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