mappoly: Genetic Linkage Maps in Autopolyploids
Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.
| Version: | 0.4.1 |
| Depends: | R (≥ 4.0.0) |
| Imports: | Rcpp (≥ 0.12.6), RcppParallel, RCurl, fields, ggpubr, ggsci, rstudioapi, plot3D, dplyr, crayon, cli, magrittr, reshape2, ggplot2, smacof, princurve, dendextend, vcfR, zoo, plotly |
| LinkingTo: | Rcpp, RcppParallel |
| Suggests: | testthat, updog, fitPoly, polymapR, AGHmatrix, gatepoints, knitr, rmarkdown, stringr |
| Published: | 2024-03-06 |
| DOI: | 10.32614/CRAN.package.mappoly |
| Author: | Marcelo Mollinari 
[aut, cre],
Gabriel Gesteira
[aut],
Cristiane Taniguti
[aut],
Jeekin Lau [aut],
Oscar Riera-Lizarazu
[ctb],
Guilhereme Pereira
[ctb],
Augusto Garcia
[ctb],
Zhao-Bang Zeng
[ctb],
Katharine Preedy [ctb, cph] (MDS ordering algorithm),
Robert Gentleman [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
Ross Ihaka [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
R Foundation [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp),
R-core [cph] (C code for MLE optimization in
src/pairwise_estimation.cpp) |
| Maintainer: | Marcelo Mollinari <mmollin at ncsu.edu> |
| BugReports: | https://github.com/mmollina/MAPpoly/issues |
| License: | GPL-3 |
| URL: | https://github.com/mmollina/MAPpoly |
| NeedsCompilation: | yes |
| SystemRequirements: | GNU make |
| Citation: | mappoly citation info |
| Materials: | README NEWS |
| In views: | Agriculture |
| CRAN checks: | mappoly results |
Documentation:
| Reference manual: | mappoly.pdf |
| Vignettes: |
mappoly_intro |
Downloads:
| Package source: | mappoly_0.4.1.tar.gz |
| Windows binaries: | r-devel: mappoly_0.4.1.zip, r-release: mappoly_0.4.1.zip, r-oldrel: mappoly_0.4.1.zip |
| macOS binaries: | r-devel (arm64): mappoly_0.4.1.tgz, r-release (arm64): mappoly_0.4.1.tgz, r-oldrel (arm64): mappoly_0.4.1.tgz, r-devel (x86_64): mappoly_0.4.1.tgz, r-release (x86_64): mappoly_0.4.1.tgz, r-oldrel (x86_64): mappoly_0.4.1.tgz |
| Old sources: | mappoly archive |
Reverse dependencies:
| Reverse imports: | qtlpoly |
| Reverse suggests: | polymapR, polyqtlR |
Linking:
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