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:Matteo Sesia [aut, cre]

SNPknock_0.8.4.tar.gz

SNPknock_0.8.4.tgz(r-4.5-x86_64)SNPknock_0.8.4.tgz(r-4.5-arm64)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

Pkgdown site:https://msesia.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

4.76 score 2 stars 29 scripts 233 downloads 27 exports 5 dependencies

Last updated 5 years agofrom:f0d027b489. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 30 2025
R-4.5-mac-x86_64	NOTE	Jan 30 2025
R-4.5-mac-aarch64	NOTE	Jan 30 2025
R-4.5-linux-x86_64	NOTE	Jan 30 2025
R-4.4-mac-x86_64	NOTE	Jan 30 2025
R-4.4-mac-aarch64	NOTE	Jan 30 2025
R-4.3-mac-x86_64	NOTE	Jan 30 2025
R-4.3-mac-aarch64	NOTE	Dec 31 2024

Exports:assemble_pEmit assemble_pEmit_phased assemble_pInit assemble_pInit_phased assemble_Q compute_Q1 fwGenotypes fwGenotypes_wrapper fwHaplotypes fwHaplotypes_wrapper fwHMM fwHMM_wrapper GroupGenotypes_wrapper GroupHaplotypes_wrapper knockoffDMC knockoffDMC_wrapper knockoffGenotypes knockoffHaplotypes knockoffHMM knockoffHMM_wrapper loadEMParameters loadHMM rand_weighted runFastPhase sampleDMC sampleHMM writeXtoInp

Dependencies:rbibutils Rcpp RcppArmadillo RcppProgress Rdpack

Using SNPknock in R

Matteo Sesia ([email protected])

Rendered fromSNPknock.Rmdusingknitr::rmarkdownon Jan 30 2025.

Last update: 2019-05-15
Started: 2019-05-01

Using SNPknock with Genetic Data

Matteo Sesia ([email protected])

Rendered fromgenotypes.Rmdusingknitr::rmarkdownon Jan 30 2025.

Last update: 2019-05-10
Started: 2019-05-01

Citation

Development and contributors

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