Package: krm 2022.10-17
krm: Kernel Based Regression Models
Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence. This package is described in Fong et al. (2015) <doi:10.1093/biostatistics/kxu056>.
Authors:
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krm.pdf |krm.html✨
krm/json (API)
| # Install 'krm' in R: |
| install.packages('krm', repos = c('https://youyifong.r-universe.dev', 'https://cloud.r-project.org')) |
- aa.prop.list - Amino Acid Properties
- cloud9 - 9-Component Mixture Dirichlet Prior for Protein Sequences
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:96e5c5c18e. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 07 2024 |
| R-4.5-win-x86_64 | OK | Sep 07 2024 |
| R-4.5-linux-x86_64 | OK | Sep 07 2024 |
| R-4.4-win-x86_64 | OK | Sep 07 2024 |
| R-4.4-mac-x86_64 | OK | Sep 07 2024 |
| R-4.4-mac-aarch64 | OK | Sep 07 2024 |
| R-4.3-win-x86_64 | OK | Sep 07 2024 |
| R-4.3-mac-x86_64 | OK | Sep 07 2024 |
| R-4.3-mac-aarch64 | OK | Sep 07 2024 |
Exports:aa2arabicalignment2countalignment2trancountarabic2arabicFilearabic2fastaFilecalcPairwiseIdentitychi.normddirichletdmdirichletfastaFile2arabicFilegetSeqKernelhmmMargLlikkrm.mostkrm.score.testlogIntegrateDirichletlogIntegrateMixDirichletmodifyDirichletrdirichletreadArabicFilereadBlockFilereadFastaFilereadPriorFromFilereadSelexAsMatrixreadSelexFileremoveGaprmdirichletselexFile2arabicFilesim.liu.2007sim.liu.2008string2arabicstringList2arabicFilewriteFastaFile
Dependencies:kyotil
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Amino Acid Properties | aa.prop.list |
| Functions Related to Sequence Alignment | alignment2count alignment2trancount calcPairwiseIdentity removeGap |
| A Transformation of Chi-squared Random Variable | chi.norm |
| 9-Component Mixture Dirichlet Prior for Protein Sequences | cloud9 |
| Functions related to mixture Dirichlet distribution | ddirichlet dmdirichlet logIntegrateDirichlet logIntegrateMixDirichlet modifyDirichlet rdirichlet rmdirichlet |
| Protein Sequence Kernels | getSeqKernel |
| Functions related to profile HMM | hmmMargLlik readPriorFromFile |
| Kernel-based Regression Models | krm |
| Kernel-based Regression Model Maximum of adjusted Score Test | krm.most |
| Adjusted Score Test | krm.score.test |
| Read a Fasta Sequence File | aa2arabic arabic2arabicFile arabic2fastaFile fastaFile2arabicFile readArabicFile readBlockFile readFastaFile readSelexAsMatrix readSelexFile selexFile2arabicFile string2arabic stringList2arabicFile writeFastaFile |
| Simulate sDataset | sim.liu.2007 sim.liu.2008 |
