Package: tripsAndDipR 0.2.0
Thomas Delomas
tripsAndDipR: Inference of Ploidy from Sequencing Data
Uses read counts for biallelic single nucleotide polymorphisms (SNPs) to infer ploidy. It allows parameters to be specified to account for sequencing error rates and allelic bias. For details of the algorithms, please see Delomas (2019) <doi:10.1111/1755-0998.13073> and Delomas et al. (2021) <doi:10.1111/1755-0998.13431>.
Authors:
tripsAndDipR_0.2.0.tar.gz
tripsAndDipR_0.2.0.zip(r-4.7-x86_64)tripsAndDipR_0.2.0.zip(r-4.7-arm64)tripsAndDipR_0.2.0.zip(r-4.6-x86_64)tripsAndDipR_0.2.0.zip(r-4.6-arm64)tripsAndDipR_0.2.0.zip(r-4.5-x86_64)
tripsAndDipR_0.2.0.tgz(r-4.6-x86_64)tripsAndDipR_0.2.0.tgz(r-4.6-arm64)tripsAndDipR_0.2.0.tgz(r-4.5-x86_64)tripsAndDipR_0.2.0.tgz(r-4.5-arm64)
tripsAndDipR_0.2.0.tar.gz(r-4.7-arm64)tripsAndDipR_0.2.0.tar.gz(r-4.7-x86_64)tripsAndDipR_0.2.0.tar.gz(r-4.6-arm64)tripsAndDipR_0.2.0.tar.gz(r-4.6-x86_64)
tripsAndDipR_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tripsAndDipR/json (API)
| # Install 'tripsAndDipR' in R: |
| install.packages('tripsAndDipR', repos = c('https://delomast.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/delomast/tripsanddipr/issues
Last updated from:291d186426. Checks:13 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 137 | ||
| linux-devel-x86_64 | WARNING | 144 | ||
| source / vignettes | OK | 180 | ||
| linux-release-arm64 | WARNING | 111 | ||
| linux-release-x86_64 | WARNING | 103 | ||
| macos-release-arm64 | WARNING | 194 | ||
| macos-release-x86_64 | WARNING | 351 | ||
| macos-oldrel-arm64 | WARNING | 194 | ||
| macos-oldrel-x86_64 | WARNING | 315 | ||
| windows-devel-arm64 | WARNING | 333 | ||
| windows-devel-x86_64 | WARNING | 141 | ||
| windows-release-arm64 | WARNING | 326 | ||
| windows-release-x86_64 | WARNING | 100 | ||
| windows-oldrel-x86_64 | WARNING | 103 | ||
| wasm-release | OK | 98 |
Exports:funkyPloidgenoPropsrPloidySamplestripsAndDip
Dependencies:Rcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calculate LLR's for a group of samples and a given set of ploidy values | funkyPloid |
| Fit the model for one ploidy | genoProps |
| simulate read counts for random samples | rPloidySamples |
| Uses read counts for biallelic SNPs to determine if a sample is diploid or triploid | tripsAndDip |