QDNAseq-package {QDNAseq} | R Documentation

## Package QDNAseq

### Description

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.

### Details

A package to detect chromosomal aberrations from whole-genome sequencing data. `QDNAseqReadCounts` and `QDNAseqCopyNumbers` classes are used as the main data structures.

### How to cite this package

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, 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.

### License

This package is licensed under GPL.

### Author(s)

Ilari Scheinin

[Package QDNAseq version 1.30.0 Index]