mappoly (version 0.4.1)

make_pairs_mappoly: 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)

Value

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

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

Author

Marcelo Mollinari,

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

    ## 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")