PSCBS-package: Package PSCBS

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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.

Installation and updates

To install this package, use install.packages("PSCBS").

To get started

To get started, see:

1. Vignettes 'Parent-specific copy-number segmentation using Paired PSCBS' and 'Total copy-number segmentation using CBS'.

2. segmentByCBS() - segments total copy-numbers, or any other unimodal genomic signals, using the CBS method [3,4].

3. segmentByPairedPSCBS() - segments allele-specific tumor signal from a tumor with a matched normal using the Paired PSCBS method [1,2].

4. segmentByNonPairedPSCBS() - segments allele-specific tumor signal from a tumor without a matched normal using the Non-Paired PSCBS method adopted from [1,2].

How to cite

Please use [1] and [2] to cite when using Paired PSCBS, and [3] and [4] when using CBS. When using Non-Paired PSCBS, please cite [1] and [2] as well.

License

GPL (>= 2).

Author(s)

Henrik Bengtsson

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

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.