mappoly (version 0.4.1)

sim_homologous: Simulate homology groups

Description

Simulate two homology groups (one for each parent) and their linkage phase configuration.

Usage

sim_homologous(ploidy, n.mrk, prob.dose = NULL, seed = NULL)

Value

a list containing the following components:

hom.allele.p

a list of vectors containing linkage phase configurations. Each vector contains the numbers of the homologous chromosomes in which the alleles are located. For instance, a vector containing \((1,3,4)\) means that the marker has three doses located in the chromosomes 1, 3 and 4. For zero doses, use 0

p

contains the indices of the starting positions of the dosages, considering that the vectors contained in p are concatenated. Markers with no doses (zero doses are also considered)

hom.allele.q

Analogously to hom.allele.p

q

Analogously to p

ploidy

ploidy level

Arguments

ploidy

ploidy level. Must be an even number

n.mrk

number of markers

prob.dose

a vector indicating the proportion of markers for different dosage to be simulated (default = NULL)

seed

random number generator seed

Author

Marcelo Mollinari,

Details

This function prevents the simulation of linkage phase configurations which are impossible to estimate via two point methods

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_. tools:::Rd_expr_doi("10.1534/g3.119.400378")

Examples

    h.temp <- sim_homologous(ploidy = 6, n.mrk = 20)