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 homologues. 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: |
0.3.1 |
| Depends: |
R (≥ 4.0.0) |
| Imports: |
Rcpp (≥ 0.12.6), RcppParallel, RCurl, fields, ggpubr, ggsci, rstudioapi, scatterplot3d, dplyr, crayon, cli, magrittr, reshape2, ggplot2, princurve, dendextend, vcfR, zoo, plotly |
| LinkingTo: |
Rcpp, RcppParallel |
| Suggests: |
smacof, testthat, updog, fitPoly, polymapR, AGHmatrix, gatepoints, knitr, rmarkdown |
| Published: |
2022-07-06 |
| Author: |
Marcelo Mollinari 
[aut, cre],
Gabriel Gesteira
[aut],
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: |
C++11, GNU make |
| Citation: |
mappoly citation info |
| Materials: |
README NEWS |
| CRAN checks: |
mappoly results |