hexafake: Simulated autohexaploid dataset.

In qtlpoly: Random-Effect Multiple QTL Mapping in Autopolyploids

Simulated autohexaploid dataset.

Description

A dataset of a hypothetical autohexaploid full-sib population containing three homology groups

Usage

hexafake

Format

An object of class mappoly.data which contains a list with the following components:

plody

ploidy level = 6

n.ind

number individuals = 300

n.mrk

total number of markers = 1500

ind.names

the names of the individuals

mrk.names

the names of the markers

dosage.p1

a vector containing the dosage in parent P for all n.mrk markers

dosage.p2

a vector containing the dosage in parent Q for all n.mrk markers

chrom

a vector indicating the chromosome each marker belongs. Zero indicates that the marker was not assigned to any chromosome

genome.pos

Physical position of the markers into the sequence

geno.dose

a matrix containing the dosage for each markers (rows) for each individual (columns). Missing data are represented by ploidy_level + 1 = 7

n.phen

There are no phenotypes in this simulation

phen

There are no phenotypes in this simulation

chisq.pval

vector containing p-values for all markers associated to the chi-square test for the expected segregation patterns under Mendelian segregation

Author(s)

Marcelo Mollinari, [e-mail]

References

Mollinari M, Garcia AAF (2019) Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models, G3: Genes|Genomes|Genetics 9 (10): 3297-3314. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/g3.119.400378")}

Examples

library(mappoly)
plot(hexafake)

qtlpoly documentation built on May 29, 2024, 2:14 a.m.