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QDNAseq: Quantitative DNA sequencing for chromosomal aberrations

This repository contains source code for the R/Bioconductor package QDNAseq. For a description, please see this article, and for usage, the vignette from Bioconductor development version or the latest release

Citing QDNAseq

To cite QDNAseq, please use:
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B (2014) DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Research 24: 2022-2032

Software quality

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Version

Version

1.8.0

License

GPL

Issues

36

Pull Requests

2

Stars

50

Forks

29

Maintainer

Daoud Sie

Last Published

February 15th, 2017

Functions in QDNAseq (1.8.0)

QDNAseqCopyNumbers

Container for QDNAseq read count data
addPhenodata

Adds phenotype data from a file to a QDNAseqReadCounts or a QDNAseqCopyNumbers object
LGG150

LGG150 chromosomes 7-10
segmentBins

Segments normalized copy number data
exportBins

Exports to a file
plot

Plot copy number profile
frequencyPlot

Plot copy number aberration frequencies
makeCgh

Constructs a 'cghRaw', 'cghSeg', or 'cghCall' object
poolRuns

Pools binned read counts across samples
createBins

Builds bin annotation data for a particular bin size
highlightFilters

Highlights data points in a plotted profile to evaluate filtering
QDNAseqSignals

A parent class for containers of QDNAseq data
applyFilters

Adjusts the filtering on which bins are used
estimateCorrection

Estimate correction to read counts for GC content and mappability
compareToReference

Divide binned read counts with those of reference samples
noisePlot

Plot noise as a function of sequence depth
QDNAseq-package

Package QDNAseq
QDNAseq-defunct

Defunct functions in package ‘QDNAseq’
getBinAnnotations

Gets bin annotation data for a particular bin size
normalizeBins

Normalizes binned read counts
smoothOutlierBins

Smooth outlier bins after normalization
binReadCounts

Calculate binned read counts from a set of BAM files
QDNAseqReadCounts

Container for QDNAseq read count data
correctBins

Correct binned read counts for GC content and mappability
normalizeSegmentedBins

Normalize segmented bins
isobarPlot

Plot median read counts as a function of GC content and mappability
callBins

Call aberrations from segmented copy number data