make_pairs_mappoly: Subset pairwise recombination fractions

In mappoly: Genetic Linkage Maps in Autopolyploids

Subset pairwise recombination fractions

Description

Get a subset of an object of class mappoly.twopt or mappoly.twopt2 (i.e. recombination fraction) and LOD score statistics for all possible linkage phase combinations based on a sequence of markers.

Usage

make_pairs_mappoly(input.twopt, input.seq)

Arguments

input.twopt	an object of class mappoly.twopt
input.seq	an object of class mappoly.sequence, with a sequence of markers contained in input.twopt

Value

an object of class mappoly.twopt which is a subset of input.twopt. See est_pairwise_rf for details

Author(s)

Marcelo Mollinari, [e-mail]

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

    ## selecting some markers along the genome
    some.mrk <- make_seq_mappoly(hexafake, seq(1, 1500, 30))
    all.pairs <- est_pairwise_rf(input.seq = some.mrk)
    mat.full <- rf_list_to_matrix(input.twopt = all.pairs)
    plot(mat.full)
    
    ## selecting two-point information for chromosome 1
    mrks.1 <- make_seq_mappoly(hexafake, names(which(some.mrk$chrom == 1)))
    p1 <- make_pairs_mappoly(input.seq = mrks.1, input.twopt = all.pairs)
    m1 <- rf_list_to_matrix(input.twopt = p1)
    plot(m1, main.text = "LG1")
   

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