mappoly: Genetic Linkage Maps in Autopolyploids

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>.

README.md Introduction to MAPpoly"

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Package details
Author	Marcelo Mollinari [aut, cre] (ORCID: <https://orcid.org/0000-0002-7001-8498>), Gabriel Gesteira [aut] (ORCID: <https://orcid.org/0000-0002-4106-7346>), Cristiane Taniguti [aut] (ORCID: <https://orcid.org/0000-0002-2021-6883>), Jeekin Lau [aut] (ORCID: <https://orcid.org/0000-0003-1114-6892>), Oscar Riera-Lizarazu [ctb] (ORCID: <https://orcid.org/0000-0002-7477-4063>), Guilherme Pereira [ctb] (ORCID: <https://orcid.org/0000-0002-7106-8630>), Augusto Garcia [ctb] (ORCID: <https://orcid.org/0000-0003-0634-3277>), Zhao-Bang Zeng [ctb] (ORCID: <https://orcid.org/0000-0002-3115-1149>), 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@proton.me>
License	GPL-3
Version	0.4.2
URL	https://github.com/mmollina/MAPpoly
Package repository	View on CRAN
Installation	Install the latest version of this package by entering the following in R: `install.packages("mappoly")`