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DESCRIPTION
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Package: mappoly
Type: Package
Title: Genetic Linkage Maps in Autopolyploids
Version: 0.4.1
Authors@R: c(person(given = "Marcelo",
family = "Mollinari",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID="0000-0002-7001-8498")),
person(given = "Gabriel",
family = "Gesteira",
role = "aut",
email = "[email protected]",
comment = c(ORCID="0000-0002-4106-7346")),
person(given = "Cristiane",
family = "Taniguti",
role = "aut",
email = "[email protected]",
comment = c(ORCID="0000-0002-2021-6883")),
person(given = "Jeekin",
family = "Lau",
role = "aut",
email = "[email protected]",
comment = c(ORCID="0000-0003-1114-6892")),
person(given = "Oscar",
family = "Riera-Lizarazu",
role = "ctb",
email = "[email protected]",
comment = c(ORCID="0000-0002-7477-4063")),
person(given = "Guilhereme",
family = "Pereira",
role = "ctb",
comment = c(ORCID="0000-0002-7106-8630")),
person(given = "Augusto",
family = "Garcia",
role = "ctb",
comment = c(ORCID="0000-0003-0634-3277")),
person(given = "Zhao-Bang",
family = "Zeng",
role = "ctb",
comment = c(ORCID="0000-0002-3115-1149")),
person(given = "Katharine",
family = "Preedy",
role = c("ctb", "cph"),
comment = "MDS ordering algorithm"),
person(given = "Robert",
family = "Gentleman",
role = "cph",
comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
person(given = "Ross",
family = "Ihaka",
role = "cph",
comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
person(given = "R Foundation",
role = "cph",
comment = "C code for MLE optimization in src/pairwise_estimation.cpp"),
person(given = "R-core",
role = "cph",
comment = "C code for MLE optimization in src/pairwise_estimation.cpp"))
Maintainer: Marcelo Mollinari <[email protected]>
Description: 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>.
License: GPL-3
LazyData: TRUE
LazyDataCompression: xz
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
RoxygenNote: 7.3.1
SystemRequirements: GNU make
Encoding: UTF-8
Suggests:
testthat,
updog,
fitPoly,
polymapR,
AGHmatrix,
gatepoints,
knitr,
rmarkdown,
stringr
URL: https://github.com/mmollina/MAPpoly
BugReports: https://github.com/mmollina/MAPpoly/issues
VignetteBuilder: knitr