Constructs genetic linkage 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).
Methods are described in Mollinari and Garcia (2019)
<doi:10.1534/g3.119.400378> and Mollinari et al. (2020)
<doi:10.1534/g3.119.400620>.
| Version: |
0.4.2 |
| Depends: |
R (≥ 4.0.0) |
| Imports: |
Rcpp (≥ 0.12.6), RcppParallel, RCurl, fields, ggpubr, ggsci, rstudioapi, dplyr, crayon, cli, magrittr, reshape2, ggplot2, smacof, princurve, dendextend, vcfR, zoo, plotly |
| LinkingTo: |
Rcpp, RcppParallel |
| Suggests: |
updog, plot3D, fitPoly, polymapR, AGHmatrix, gatepoints, knitr, rmarkdown, stringr |
| Published: |
2026-01-12 |
| DOI: |
10.32614/CRAN.package.mappoly |
| Author: |
Marcelo Mollinari 
[aut, cre],
Gabriel Gesteira
[aut],
Cristiane Taniguti
[aut],
Jeekin Lau [aut],
Oscar Riera-Lizarazu
[ctb],
Guilherme 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 Core Team [cph] (Portions of C/C++ code adapted from R sources; see
src/pairwise_estimation.cpp),
R Foundation for Statistical Computing [cph] (Portions of C/C++ code
adapted from R sources; see src/pairwise_estimation.cpp) |
| Maintainer: |
Marcelo Mollinari <marcelo.mollinari at proton.me> |
| 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 |
| CRAN checks: |
mappoly results |