Package: dcifer 1.3.0
Inna Gerlovina
dcifer: Genetic Relatedness Between Polyclonal Infections
An implementation of Dcifer (Distance for complex infections: fast estimation of relatedness), an identity by descent (IBD) based method to calculate genetic relatedness between polyclonal infections from biallelic and multiallelic data. The package includes functions that format and preprocess the data, implement the method, and visualize the results. Gerlovina et al. (2022) <doi:10.1093/genetics/iyac126>.
Authors:
dcifer_1.3.0.tar.gz
dcifer_1.3.0.zip(r-4.5)dcifer_1.3.0.zip(r-4.4)dcifer_1.3.0.zip(r-4.3)
dcifer_1.3.0.tgz(r-4.5-x86_64)dcifer_1.3.0.tgz(r-4.5-arm64)dcifer_1.3.0.tgz(r-4.4-x86_64)dcifer_1.3.0.tgz(r-4.4-arm64)dcifer_1.3.0.tgz(r-4.3-x86_64)dcifer_1.3.0.tgz(r-4.3-arm64)
dcifer_1.3.0.tar.gz(r-4.5-noble)dcifer_1.3.0.tar.gz(r-4.4-noble)
dcifer_1.3.0.tgz(r-4.4-emscripten)dcifer_1.3.0.tgz(r-4.3-emscripten)
dcifer.pdf |dcifer.html✨
dcifer/json (API)
NEWS
| # Install 'dcifer' in R: |
| install.packages('dcifer', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/eppicenter/dcifer/issues
Pkgdown site:https://eppicenter.github.io
Last updated 9 months agofrom:ac888d189c. Checks:11 OK. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 30 2025 |
| R-4.5-win-x86_64 | OK | Jan 30 2025 |
| R-4.5-mac-x86_64 | OK | Jan 30 2025 |
| R-4.5-mac-aarch64 | OK | Jan 30 2025 |
| R-4.5-linux-x86_64 | OK | Jan 30 2025 |
| R-4.4-win-x86_64 | OK | Jan 30 2025 |
| R-4.4-mac-x86_64 | OK | Jan 30 2025 |
| R-4.4-mac-aarch64 | OK | Jan 30 2025 |
| R-4.3-win-x86_64 | OK | Jan 30 2025 |
| R-4.3-mac-x86_64 | OK | Jan 30 2025 |
| R-4.3-mac-aarch64 | OK | Jan 30 2025 |
Exports:calcAfreqformatAfreqformatDatgenerateRevalgetCOIibdDatibdEstMibdPairlogRevalmatchAfreqplotColorbarplotRelprobUxUyreadAfreqreadDat
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate Allele Frequencies | calcAfreq |
| Dcifer results | dres |
| Sample data | dsmp |
| Read and Reformat Data | format formatAfreq formatDat readAfreq readDat |
| Grid of Parameter Values | generateReval |
| Calculate COI | getCOI |
| Pairwise Relatedness | ibdDat |
| Estimate Relatedness and a Number of Related Strains | ibdEstM |
| Relatedness Between Two Samples | ibdPair |
| Logarithms of 'reval' | logReval |
| Match Samples and Allele Frequencies | matchAfreq |
| Colorbar | plotColorbar |
| Plot Relatedness Estimates | plotRel |
| Likelihood for U_x, U_y | probUxUy |
| Parameter grid | revals |
