Package: uncertR 0.1.3
Tanay Belapurkar
uncertR: Bootstrap Prediction Uncertainty and Its Biological Drivers in Gene-Expression Models
Fits bootstrap ensembles of penalized regression models on bulk gene-expression data, derives per-sample uncertainty scores from out-of-bag predictions, and tests whether technical covariates explain that uncertainty. The bootstrap method is described by Efron and Tibshirani (1993, ISBN:9780412042317), and elastic-net regression follows Friedman, Hastie, and Tibshirani (2010) <doi:10.18637/jss.v033.i01>. The optional immunedeconv package, used for immune-cell deconvolution, is available from GitHub <https://github.com/omnideconv/immunedeconv>.
Authors:
uncertR_0.1.3.tar.gz
uncertR_0.1.3.zip(r-4.7-any)uncertR_0.1.3.zip(r-4.6-any)
uncertR_0.1.3.tar.gz(r-4.7-any)uncertR_0.1.3.tar.gz(r-4.6-any)
uncertR_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
uncertR/json (API)
| # Install 'uncertR' in R: |
| install.packages('uncertR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:f5ba096a75. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 125 | ||
| source / vignettes | OK | 232 | ||
| linux-release | OK | 135 | ||
| windows-devel | OK | 114 | ||
| windows-release | OK | 122 | ||
| wasm-release | OK | 113 |
Exports:boot_uncertaintyclr_transformcollapse_rare_levelstumor_covariatesuncertainty_driversuncertainty_scorevalidate_uncertainty
Dependencies:codetoolsforeachfuturefuture.applyglmnetglobalsiteratorslatticelistenvMatrixparallellyRcppRcppEigenshapesurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Bootstrap ensemble with out-of-bag predictions | boot_uncertainty |
| Centered log-ratio transform for compositional fractions | clr_transform |
| Collapse rare factor levels | collapse_rare_levels |
| Assemble covariates that may drive uncertainty | tumor_covariates |
| Which covariates explain prediction uncertainty? | uncertainty_drivers |
| Per-sample uncertainty score from OOB predictions | uncertainty_score |
| Does the uncertainty score track real error? | validate_uncertainty |