Package: epoc 0.2.6-1.1
Tobias Abenius
epoc: Endogenous Perturbation Analysis of Cancer
Estimates sparse matrices A or G using fast lasso regression from mRNA transcript levels Y and CNA profiles U. Two models are provided, EPoC A where AY + U + R = 0 and EPoC G where Y = GU + E, the matrices R and E are so far treated as noise. For details see the manual page of 'lassoshooting' and the article Rebecka Jörnsten, Tobias Abenius, Teresia Kling, Linnéa Schmidt, Erik Johansson, Torbjörn E M Nordling, Bodil Nordlander, Chris Sander, Peter Gennemark, Keiko Funa, Björn Nilsson, Linda Lindahl, Sven Nelander (2011) <doi:10.1038/msb.2011.17>.
Authors:
epoc_0.2.6-1.1.tar.gz
epoc_0.2.6-1.1.tar.gz(r-4.5-noble)epoc_0.2.6-1.1.tar.gz(r-4.4-noble)
epoc_0.2.6-1.1.tgz(r-4.4-emscripten)epoc_0.2.6-1.1.tgz(r-4.3-emscripten)
epoc.pdf |epoc.html✨
epoc/json (API)
| # Install 'epoc' in R: |
| install.packages('epoc', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- synth - Blinded cancer mRNA, CNA and survival data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 years agofrom:f580787c99. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-linux | NOTE | Nov 13 2024 |
Exports:as.graph.EPOCAas.graph.EPOCGepoc.bootplotepoc.bootstrapepoc.finalepoc.lambdamaxepoc.survivalepoc.svdepoc.svdplotepoc.validationepocAepocGmodelselPlotplapplyplot.bootsizewrite.sif
Dependencies:elasticnetirrlarslassoshootinglatticelpSolveMatrixsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| EPoC | as.graph.EPOCA as.graph.EPOCG coef.EPOCA coef.EPOCG epoc epoc.lambdamax epocA epocG predict.EPOCA predict.EPOCG print.EPOCA print.EPOCG summary.EPOCA summary.EPOCG write.sif |
| epoc.bootstrap | epoc.bootplot epoc.bootstrap epoc.final plot.bootsize |
| epoc.survival | epoc.survival epoc.svd epoc.svdplot plot.EPoC.survival print.summary.EPoC.survival summary.EPoC.survival |
| epoc.validation | epoc.validation |
| Plot BIC, Mallow's Cp and lambda | modelselPlot plot.EPOCA plot.EPOCG |
| Parallell list apply | plapply |
| Plot model validation criteria | plot.EPoC.validation plot.EPoC.validation.pred plot.EPoC.validation.W |
| Blinded cancer mRNA, CNA and survival data | synth |