Package: QDNAseq 1.43.0

Daoud Sie

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.

Authors:Ilari Scheinin [aut], Daoud Sie [aut, cre], Henrik Bengtsson [aut], Erik van Dijk [ctb]

QDNAseq_1.43.0.tar.gz
QDNAseq_1.43.0.zip(r-4.5)QDNAseq_1.43.0.zip(r-4.4)QDNAseq_1.43.0.zip(r-4.3)
QDNAseq_1.43.0.tgz(r-4.4-any)QDNAseq_1.43.0.tgz(r-4.3-any)
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QDNAseq.pdf |QDNAseq.html✨
QDNAseq/json (API)
NEWS

# Install 'QDNAseq' in R:

install.packages('QDNAseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ccagc/qdnaseq/issues

Datasets:

LGG150 - LGG150 chromosomes 7-10

On BioConductor:QDNAseq-1.43.0(bioc 3.21)QDNAseq-1.42.0(bioc 3.20)

copynumbervariation dnaseq genetics genomeannotation preprocessing qualitycontrol sequencing

10.09 score 47 stars 4 packages 180 scripts 654 downloads 31 mentions 28 exports 50 dependencies

Last updated 20 days agofrom:2221207a22. Checks:OK: 3 NOTE: 2 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:addPhenodata applyFilters binReadCounts bpend bpstart calculateBlacklist calculateBlacklistByRegions calculateMappability callBins chromosomes compareToReference correctBins createBins estimateCorrection exportBins frequencyPlot getBinAnnotations highlightFilters isobarPlot iterateResiduals makeCgh noisePlot normalizeBins normalizeSegmentedBins plot poolRuns segmentBins smoothOutlierBins

Dependencies:askpass BH Biobase BiocGenerics BiocParallel Biostrings bitops CGHbase CGHcall codetools cpp11 crayon curl digest DNAcopy formatR futile.logger futile.options future future.apply GenomeInfoDb GenomeInfoDbData GenomicRanges globals httr impute IRanges jsonlite lambda.r limma listenv marray matrixStats mime openssl parallelly R.methodsS3 R.oo R.utils R6 Rhtslib Rsamtools S4Vectors snow snowfall statmod sys UCSC.utils XVector zlibbioc

Introduction to QDNAseq

Rendered fromQDNAseq.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2021-10-16
Started: 2014-03-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Package QDNAseq	QDNAseq-package QDNAseq
Adds phenotype data from a file to a QDNAseqReadCounts or a QDNAseqCopyNumbers object	addPhenodata
Adjusts the filtering on which bins are used	applyFilters applyFilters,QDNAseqReadCounts-method
Calculate binned read counts from a set of BAM files	binReadCounts
Call aberrations from segmented copy number data	callBins callBins,QDNAseqCopyNumbers-method
Divide binned read counts with those of reference samples	compareToReference compareToReference,QDNAseqCopyNumbers,numeric-method
Correct binned read counts for GC content and mappability	correctBins correctBins,QDNAseqReadCounts-method
Builds bin annotation data for a particular bin size	calculateBlacklist calculateBlacklistByRegions calculateMappability createBins iterateResiduals
Estimate correction to read counts for GC content and mappability	estimateCorrection estimateCorrection,QDNAseqReadCounts-method
Exports to a file	exportBins exportBins,QDNAseqSignals-method
Plot copy number aberration frequencies	frequencyPlot frequencyPlot,QDNAseqCopyNumbers,missing-method
Gets bin annotation data for a particular bin size	getBinAnnotations
Highlights data points in a plotted profile to evaluate filtering	highlightFilters highlightFilters,QDNAseqSignals-method
Plot median read counts as a function of GC content and mappability	isobarPlot isobarPlot,QDNAseqReadCounts,missing-method
LGG150 chromosomes 7-10	LGG150
Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object	makeCgh makeCgh,QDNAseqCopyNumbers-method
Plot noise as a function of sequence depth	noisePlot noisePlot,QDNAseqReadCounts,missing-method
Normalizes binned read counts	normalizeBins normalizeBins,QDNAseqCopyNumbers-method
Normalize segmented bins	normalizeSegmentedBins normalizeSegmentedBins,QDNAseqCopyNumbers-method
Plot copy number profile	plot plot,QDNAseqSignals,missing-method
Pools binned read counts across samples	poolRuns poolRuns,QDNAseqSignals,character-method
Defunct functions in package 'QDNAseq'	downloadBinAnnotations
Container for QDNAseq read count data	QDNAseqCopyNumbers QDNAseqCopyNumbers-class
Container for QDNAseq read count data	QDNAseqReadCounts QDNAseqReadCounts-class
A parent class for containers of QDNAseq data	bpend,QDNAseqSignals-method bpstart,QDNAseqSignals-method chromosomes,QDNAseqSignals-method QDNAseqSignals QDNAseqSignals-class
Segments normalized copy number data	segmentBins segmentBins,QDNAseqCopyNumbers-method
Smooth outlier bins after normalization	smoothOutlierBins smoothOutlierBins,QDNAseqCopyNumbers-method