CRAN/E | mappoly

mappoly

Genetic Linkage Maps in Autopolyploids

Installation

About

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.

Citation mappoly citation info
github.com/mmollina/MAPpoly
System requirements GNU make
Bug report File report

Key Metrics

Version 0.4.0
R ≥ 4.0.0
Published 2024-02-17 40 days ago
Needs compilation? yes
License GPL-3
CRAN checks mappoly results

Downloads

Yesterday 766 -2%
Last 7 days 1.686 +1282%
Last 30 days 2.121 +347%
Last 90 days 3.067 +246%
Last 365 days 5.869 +30%

Maintainer

Maintainer

Marcelo Mollinari

mmollin@ncsu.edu

Authors

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)

Material

README
NEWS
Reference manual
Package source

In Views

Agriculture

Vignettes

mappoly_intro

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

mappoly archive

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

Suggests

testthat
updog
fitPoly
polymapR
AGHmatrix
gatepoints
knitr
rmarkdown
stringr

LinkingTo

Rcpp
RcppParallel

Reverse Suggests

polymapR
polyqtlR
qtlpoly