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.
You can install jointseg from github with:
# install.packages("devtools") devtools::install_github("mpierrejean/jointseg")
The main high-level joint segmentation functions are:
jointSegfor arbitrary signals, see
PSSegfor bivariate copy-number signals, see
We also refer to
vignette("dataGeneration") for a description of the generation of synthetic DNA copy-number profiles using data from the
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.
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