Joint Segmentation of Multivariate (Copy Number) Signals

Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) .

jointseg

This package implements functions to quickly segment multivariate signals into piecewise-constant profiles, as well as a framework to generate realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies.

Installation

You can install jointseg from github with:

# install.packages("devtools")
devtools::install_github("mpierrejean/jointseg")

Usage

The main high-level joint segmentation functions are:

jointSeg for arbitrary signals, see ?jointSeg.
PSSeg for bivariate copy-number signals, see ?PSSeg and vignette("PSSeg").

We also refer to vignette("dataGeneration") for a description of the generation of synthetic DNA copy-number profiles using data from the acnr package.

References

Pierre-Jean, M, Rigaill, G. J. and Neuvial, P. (2015). "Performance Evaluation of DNA Copy Number Segmentation Methods." Briefings in Bioinformatics, no. 4: 600–615.