PSCBS-package: Package PSCBS

Description

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported..

This package should be considered to be in an alpha or beta phase. You should expect the API to be changing over time.

Arguments

Requirements

This package requires external packages R.utils (>= 1.26.2), utils, R.methodsS3 (>= 1.4.4), R.oo (>= 1.13.9), R.utils (>= 1.26.2), DNAcopy (>= 1.27.2), R.rsp (>= 0.9.17), and also suggests DNAcopy (>= 1.27.2), aroma.light (>= 1.28.0), matrixStats (>= 0.8.5), R.cache (>= 0.7.1), Hmisc (>= 3.12-2), ggplot2 (>= 0.9.3.1), R.devices (>= 2.5.0), R.rsp (>= 0.9.17).

Installation and updates

To install this package, use install.packages("PSCBS"). Inorder to run examples, also install.packages("PSCBS.data").

To get started

To get started, see:

segmentByCBS() - segments total copy-numbers, or any other unimodal genomic signals, using the CBS method [3,4].
segmentByPairedPSCBS() - segments allele-specific tumor signal from a tumor with a matched normal using the Paired PSCBS method [1,2].

How to cite

Please use [1] and [2] to cite when using Paired PSCBS, and [3] and [4] when using CBS.

License

GPL (>= 2).

References

[1] A.B. Olshen, H. Bengtsson, P. Neuvial, P.T. Spellman, R.A. Olshen, V.E. Seshan, Parent-specific copy number in paired tumor-normal studies using circular binary segmentation, Bioinformatics, 2011 [2] H. Bengtsson, P. Neuvial and T.P. Speed, TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays, BMC Bioinformatics, 2010 [3] A.B. Olshen, E.S. Venkatraman (aka Venkatraman E. Seshan), R. Lucito and M. Wigler, Circular binary segmentation for the analysis of array-based DNA copy number data, Biostatistics, 2004 [4] E.S. Venkatraman and A.B. Olshen, A faster circular binary segmentation algorithm for the analysis of array CGH data, Bioinformatics, 2007