mappoly: Genetic Linkage Maps in Autopolyploids (original) (raw)

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
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

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