mappoly (v. 0.1.0) is an under development R package to construct genetic maps in autopolyploids with even ploidy levels. In its current version, mappoly can handle ploidy levels up to 8 when using hidden Markov models (HMM), and up to 12 when using the two-point simplification. All the two-point based functions are fast enough to run on standard computers. However, we strongly recommend to use high-performance computation for HMM-based analysis, especially for ploidy levels higher than 4.
We assume the genotypic data is available and in the format required by mappoly. In a future version, this document will include instructions about genotype calling and vcf files. The derivation of the HMM used in mappoly can be found in Mollinari and Garcia 2018.
mappoly is not available in CRAN, but you can install it from Git Hub. Within R, you need to install and load the package devtools:
install.packages("devtools")To install mappoly from Git Hub use
devtools::install_github("mmollina/mappoly")- Building a genetic map in an hexaploid full-sib population using MAPpoly
- Building a genetic map using potato genotype data from SolCAP
This package has been developed as part of the Genomic Tools for Sweetpotato Improvement project (GT4SP), funded by Bill & Melinda Gates Foundation.