Package: SNPknock 0.8.4
Matteo Sesia
SNPknock: Knockoffs for Hidden Markov Models and Genetic Data
Generate knockoffs for genetic data and hidden Markov models. For more information, see the website below and the accompanying papers: "Gene hunting with hidden Markov model knockoffs", Sesia et al., Biometrika, 2019, (<doi:10.1093/biomet/asy033>). "Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, (<doi:10.1101/631390>).
Authors:
SNPknock_0.8.4.tar.gz
SNPknock_0.8.4.tgz(r-4.4-x86_64)SNPknock_0.8.4.tgz(r-4.4-arm64)SNPknock_0.8.4.tgz(r-4.3-x86_64)SNPknock_0.8.4.tgz(r-4.3-arm64)
SNPknock_0.8.4.tar.gz(r-4.5-noble)SNPknock_0.8.4.tar.gz(r-4.4-noble)
SNPknock_0.8.4.tgz(r-4.4-emscripten)SNPknock_0.8.4.tgz(r-4.3-emscripten)
SNPknock.pdf |SNPknock.html✨
SNPknock/json (API)
NEWS
| # Install 'SNPknock' in R: |
| install.packages('SNPknock', repos = c('https://msesia.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/msesia/snpknock/issues
Last updated 5 years agofrom:f0d027b489. Checks:OK: 1 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 01 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 01 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 01 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 01 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 01 2024 |
Exports:assemble_pEmitassemble_pEmit_phasedassemble_pInitassemble_pInit_phasedassemble_Qcompute_Q1fwGenotypesfwGenotypes_wrapperfwHaplotypesfwHaplotypes_wrapperfwHMMfwHMM_wrapperGroupGenotypes_wrapperGroupHaplotypes_wrapperknockoffDMCknockoffDMC_wrapperknockoffGenotypesknockoffHaplotypesknockoffHMMknockoffHMM_wrapperloadEMParametersloadHMMrand_weightedrunFastPhasesampleDMCsampleHMMwriteXtoInp
Dependencies:rbibutilsRcppRcppArmadilloRcppProgressRdpack
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Forward-backward sampling for hidden Markov models for genotypes | fwGenotypes |
| Forward-backward sampling for hidden Markov models for haplotypes | fwHaplotypes |
| Forward-backward sampling for hidden Markov models | fwHMM |
| Group knockoffs of discrete Markov chains | knockoffDMC |
| Group-knockoffs of unphased genotypes | knockoffGenotypes |
| Group-knockoffs of phased haplotypes | knockoffHaplotypes |
| Group knockoffs of hidden Markov models | knockoffHMM |
| Load HMM parameters fitted by fastPHASE | loadHMM |
| Fit an HMM to genetic data using fastPHASE | runFastPhase |
| Sample discrete Markov chains | sampleDMC |
| Sample hidden Markov models | sampleHMM |
| Convert genotypes X into the fastPHASE input format | writeXtoInp |