Package: PeakSegOptimal 2024.10.1

PeakSegOptimal: Optimal Segmentation Subject to Up-Down Constraints

Computes optimal changepoint models using the Poisson likelihood for non-negative count data, subject to the PeakSeg constraint: the first change must be up, second change down, third change up, etc. For more info about the models and algorithms, read "Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection" <https://jmlr.org/papers/v21/18-843.html> by TD Hocking et al.

Authors:Toby Dylan Hocking [aut, cre]

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PeakSegOptimal.pdf |PeakSegOptimal.html
PeakSegOptimal/json (API)
NEWS

# Install 'PeakSegOptimal' in R:
install.packages('PeakSegOptimal', repos = c('https://tdhock.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tdhock/peaksegoptimal/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

3.33 score 6 stars 36 scripts 433 downloads 7 exports 30 dependencies

Last updated 2 months agofrom:d20f3a37bb. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-win-x86_64OKNov 01 2024
R-4.5-linux-x86_64OKNov 01 2024
R-4.4-win-x86_64OKNov 01 2024
R-4.4-mac-x86_64OKNov 01 2024
R-4.4-mac-aarch64OKNov 01 2024
R-4.3-win-x86_64OKNov 01 2024
R-4.3-mac-x86_64OKNov 01 2024
R-4.3-mac-aarch64OKNov 01 2024

Exports:oracleModelComplexityPeakSegFPOPPeakSegFPOPchromPeakSegPDPAPeakSegPDPAchromPeakSegPDPAInfPoissonLoss

Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepenaltyLearningpillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
H3K4me3_PGP_immune ChIP-seq data set chunk 24H3K4me3_PGP_immune_chunk24
H3K4me3_XJ_immune chunk 1H3K4me3_XJ_immune_chunk1
oracleModelComplexityoracleModelComplexity
PeakSegFPOPPeakSegFPOP
PeakSegFPOPchromPeakSegFPOPchrom
PeakSegPDPAPeakSegPDPA
PeakSegPDPAchromPeakSegPDPAchrom
PeakSegPDPAInfPeakSegPDPAInf
PoissonLossPoissonLoss