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Package: cpam 0.2.1
cpam: Changepoint Additive Models for Time Series Omics Data
Provides a comprehensive framework for time series omics analysis, integrating changepoint detection, smooth and shape-constrained trends, and uncertainty quantification. It supports gene- and transcript-level inferences, p-value aggregation for improved power, and both case-only and case-control designs. It includes an interactive 'shiny' interface. The methods are described in Yates et al. (2024) <doi:10.1101/2024.12.22.630003>.
Authors:
cpam_0.2.1.tar.gz
cpam_0.2.1.zip(r-4.7-any)cpam_0.2.1.zip(r-4.6-any)cpam_0.2.1.zip(r-4.5-any)
cpam_0.2.1.tgz(r-4.6-any)cpam_0.2.1.tgz(r-4.5-any)
cpam_0.2.1.tar.gz(r-4.7-any)cpam_0.2.1.tar.gz(r-4.6-any)
cpam_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cpam/json (API)
| # Install 'cpam' in R: |
| install.packages('cpam', repos = c('https://l-a-yates.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/l-a-yates/cpam/issues
Pkgdown/docs site:https://l-a-yates.github.io
Last updated from:9ebd3295f5. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 140 | ||
| source / vignettes | OK | 278 | ||
| linux-release | OK | 165 | ||
| macos-release | OK | 104 | ||
| macos-oldrel | OK | 151 | ||
| windows-devel | OK | 135 | ||
| windows-release | OK | 119 | ||
| windows-oldrel | OK | 122 | ||
| wasm-release | OK | 106 |
Exports:%>%acatcompute_p_valuesestimate_changepointlancasterplot_clusterplot_cpamprepare_cpamresultsselect_shapets_filtervisualise
Dependencies:base64encBHbslibcachemclicommonmarkcpp11digestdplyredgeRfarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvisobandjquerylibjsonlitelabelinglaterlatticelifecyclelimmalocfitmagrittrMatrixmatrixStatsmemoisemgcvmimemvnfastnlmeotelpbmcapplypillarpkgconfigpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangS7sassscalesscamshinyshinyjssourcetoolsstatmodstringistringrtibbletidyrtidyselecttximportutf8vctrsviridisLitewithrxtable
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregated Cauchy Association Test | acat |
| Compute p-values for each target ID | compute_p_values |
| The cpam class | cpam cpam-class |
| Use model selection to estimate changepoints | estimate_changepoint |
| Lancaster's method for p-value aggregation | lancaster |
| Plot clustered targets | plot_cluster |
| Plot fitted changepoint additive models | plot_cpam |
| Prepare a cpam object | prepare_cpam |
| Create a results table from a cpam object | results |
| Use model selection to select a shape for each target | select_shape |
| Removes lowly expressed genes | ts_filter |
| Launches a Shiny app to visualise the data and fitted models of a cpam object | visualise visualize |