elim_redundant: Eliminate redundant markers
In mappoly: Genetic Linkage Maps in Autopolyploids

elim_redundant

R Documentation

Eliminate redundant markers

Description

Eliminate markers with identical dosage information for all individuals.

Usage

elim_redundant(input.seq, data = NULL)

Arguments

`input.seq`	an object of class `mappoly.sequence`
`data`	name of the dataset that contains sequence markers (optional, default = NULL)

Value

An object of class mappoly.unique.seq which is a list containing the following components:

`unique.seq`	an object of class `mappoly.sequence` with the redundant markers removed
`kept`	a vector containing the name of the informative markers
`eliminated`	a vector containing the name of the non-informative (eliminated) markers

Author(s)

Marcelo Mollinari, mmollin@ncsu.edu, with minor modifications by Gabriel Gesteira, gdesiqu@ncsu.edu

References

Mollinari, M., and Garcia, A. A. F. (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, _G3: Genes, Genomes, Genetics_. doi: 10.1534/g3.119.400378

Examples

    all.mrk <- make_seq_mappoly(hexafake, 'all')
    red.mrk <- elim_redundant(all.mrk)
    plot(red.mrk)
    unique.mrks <- make_seq_mappoly(red.mrk)

mappoly documentation built on Jan. 6, 2023, 1:16 a.m.