QDNAseq: Quantitative DNA sequencing for chromosomal aberrations
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorIlari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut]
Bioconductor views CopyNumberVariation DNASeq Genetics GenomeAnnotation Preprocessing QualityControl Sequencing
Date of publicationNone
MaintainerDaoud Sie <d.sie@vumc.nl>
LicenseGPL
Version1.12.0
URL https://github.com/ccagc/QDNAseq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QDNAseq")

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

LGG150 Man page
QDNAseq Man page
QDNAseq-package Man page
QDNAseqCopyNumbers Man page
QDNAseqCopyNumbers-class Man page
QDNAseqReadCounts Man page
QDNAseqReadCounts-class Man page
QDNAseqSignals Man page
QDNAseqSignals-class Man page
addPhenodata Man page Source code
applyFilters Man page
applyFilters,QDNAseqReadCounts-method Man page
betterCall Source code
binReadCounts Man page Source code
binReadCountsPerChunk Source code
binReadCountsPerSample Source code
bpend,QDNAseqSignals-method Man page
bpstart,QDNAseqSignals-method Man page
calculateBlacklist Man page Source code
calculateBlacklistByRegions Man page Source code
calculateMappability Man page Source code
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 Source code
downloadBinAnnotations Man page
estimateCorrection Man page
estimateCorrection,QDNAseqReadCounts-method Man page
expectedVariance Source code
exportBins Man page Source code
exportBins,QDNAseqSignals-method Man page
exportSEG Source code
exportVCF Source code
fapply Source code
flapply Source code
frequencyPlot Man page
frequencyPlot,QDNAseqCopyNumbers,missing-method Man page
getBinAnnotations Man page Source code
highlightFilters Man page
highlightFilters,QDNAseqSignals-method Man page
importReadCounts Source code
isobarPlot Man page
isobarPlot,QDNAseqReadCounts,missing-method Man page
iterateResiduals Man page Source code
log2adhoc Source code
log2offset Source code
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
sdDiffTrim Source code
segmentBins Man page
segmentBins,QDNAseqCopyNumbers-method Man page
smoothOutlierBins Man page
smoothOutlierBins,QDNAseqCopyNumbers-method Man page
sqrtadhoc Source code
sqrtfactor Source code
sqrtoffset Source code
vmsg Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/998.LGG150.R
R/999.package.R
R/AllClasses.R
R/AllGenerics.R
R/QDNAseqCopyNumbers-accessors.R
R/QDNAseqReadCounts-accessors.R
R/QDNAseqSignals-accessors.R
R/addPhenodata.R
R/applyFilters.R
R/binReadCounts.R
R/callBins.R
R/compareToReference.R
R/correctBins.R
R/createBinAnnotations.R
R/estimateCorrection.R
R/exportBins.R
R/getBinAnnotations.R
R/highlightFilters.R
R/logTransform.R
R/makeCgh.R
R/normalizeBins.R
R/normalizeSegmentedBins.R
R/plot-methods.R
R/poolRuns.R
R/sdDiffTrim.R
R/segmentBins.R
R/smoothOutlierBins.R
R/utils.R
R/vmsg.R
build
build/vignette.rds
data
data/LGG150.rda
inst
inst/CITATION
inst/doc
inst/doc/QDNAseq.R
inst/doc/QDNAseq.Rnw
inst/doc/QDNAseq.pdf
man
man/LGG150.Rd
man/QDNAseq-defunct.Rd
man/QDNAseq-package.Rd
man/QDNAseqCopyNumbers.Rd
man/QDNAseqReadCounts.Rd
man/QDNAseqSignals.Rd
man/addPhenodata.Rd
man/applyFilters.Rd
man/binReadCounts.Rd
man/callBins.Rd
man/compareToReference.Rd
man/correctBins.Rd
man/createBins.Rd
man/estimateCorrection.Rd
man/exportBins.Rd
man/frequencyPlot.Rd
man/getBinAnnotations.Rd
man/highlightFilters.Rd
man/isobarPlot.Rd
man/makeCgh.Rd
man/noisePlot.Rd
man/normalizeBins.Rd
man/normalizeSegmentedBins.Rd
man/plot.Rd
man/poolRuns.Rd
man/segmentBins.Rd
man/smoothOutlierBins.Rd
tests
tests/QDNAseq,reproducibility.R
tests/QDNAseq.R
vignettes
vignettes/QDNAseq.Rnw
QDNAseq documentation built on May 20, 2017, 9:45 p.m.