Package: BioMark 0.4.5
BioMark: Find Biomarkers in Two-Class Discrimination Problems
Variable selection methods are provided for several classification methods: the lasso/elastic net, PCLDA, PLSDA, and several t-tests. Two approaches for selecting cutoffs can be used, one based on the stability of model coefficients under perturbation, and the other on higher criticism.
Authors:
BioMark_0.4.5.tar.gz
BioMark_0.4.5.zip(r-4.5)BioMark_0.4.5.zip(r-4.4)BioMark_0.4.5.zip(r-4.3)
BioMark_0.4.5.tgz(r-4.4-any)BioMark_0.4.5.tgz(r-4.3-any)
BioMark_0.4.5.tar.gz(r-4.5-noble)BioMark_0.4.5.tar.gz(r-4.4-noble)
BioMark_0.4.5.tgz(r-4.4-emscripten)BioMark_0.4.5.tgz(r-4.3-emscripten)
BioMark.pdf |BioMark.html✨
BioMark/json (API)
NEWS
| # Install 'BioMark' in R: |
| install.packages('BioMark', repos = c('https://rwehrens.r-universe.dev', 'https://cloud.r-project.org')) |
- SpikeNeg - Spike-in metabolomics data for apple extracts
- SpikePos - Spike-in metabolomics data for apple extracts
- neg.markers - Spike-in metabolomics data for apple extracts
- pos.markers - Spike-in metabolomics data for apple extracts
- spikedApples - Metabolomics data on spiked apples
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 9 years agofrom:bf21eb0c77. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | NOTE | Aug 24 2024 |
| R-4.5-linux | NOTE | Aug 24 2024 |
| R-4.4-win | NOTE | Aug 24 2024 |
| R-4.4-mac | NOTE | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
Exports:AUCbiom.optionsgen.datagen.data2get.biomget.segmentsHCthreshROCroc.valuescalefunselectiontraceplot
Dependencies:codetoolscorpcorentropyfdrtoolforeachglmnetiteratorslatticeMASSMatrixplsRcppRcppEigensdashapestsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Auxiliary functions in the biomarker package | aux.biom lasso.coef lasso.stab pcr.coef pcr.stab pls.coef pls.stab pval.pcr pval.plsvip shrinkt.coef shrinkt.stab studentt.coef studentt.stab vip.coef vip.stab |
| Set or return options for stability-based biomarker selection | biom.options |
| Simulate data sets | gen.data gen.data2 |
| Get biomarkers discriminating between two classes | coef.BMark get.biom print.BMark summary.BMark |
| Subsampling segments | get.segments |
| Biomarker thresholding by Higher Criticism | HCthresh |
| ROC curves | AUC identify.ROC lines.ROC plot.ROC points.ROC print.ROC ROC ROC.default roc.value |
| Different forms of scaling | scalefun |
| Accessor function to the selected variables of a BioMark object | selection |
| Spike-in metabolomics data for apple extracts | neg.markers pos.markers SpikedApple SpikeNeg SpikePos |
| Metabolomics data on spiked apples | spikedApples |
| Plot the coefficient or stability trace for the lasso/elastic net biomarker selection. | traceplot |
