QDNAseq-package

QDNAseq


    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.


package

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.

Daoud Sie

Quantitative DNA sequencing for chromosomal aberrations

QDNAseq-package function

A package to detect chromosomal aberrations from whole-genome sequencing
    data. <code><a rd-options="" href="/link/QDNAseqReadCounts?package=QDNAseq&version=1.8.0" data-mini-rdoc="QDNAseq::QDNAseqReadCounts">QDNAseqReadCounts</a></code> and <code><a rd-options="" href="/link/QDNAseqCopyNumbers?package=QDNAseq&version=1.8.0" data-mini-rdoc="QDNAseq::QDNAseqCopyNumbers">QDNAseqCopyNumbers</a></code> classes are
    used as the main data structures.

Details

Whenever using this package, please cite:
    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*,
pp. 2022-2032.

How to cite this package

License

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.

QDNAseq-package: Package QDNAseq

Description

Arguments

Details

How to cite this package

License