mappoly (version 0.4.1)

make_mat_mappoly: Subset recombination fraction matrices

Description

Get a subset of an object of class mappoly.rf.matrix, i.e. recombination fraction and LOD score matrices based in a sequence of markers.

Usage

make_mat_mappoly(input.mat, input.seq)

Value

an object of class mappoly.rf.matrix, which is a subset of 'input.mat'. See rf_list_to_matrix for details

Arguments

input.mat

an object of class mappoly.rf.matrix

input.seq

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

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

    # sequence with 20 markers
    mrk.seq <- make_seq_mappoly(hexafake, 1:20)
    mrk.pairs <- est_pairwise_rf(input.seq = mrk.seq,
                               verbose = TRUE)
    ## Full recombination fraction matrix
    mat <- rf_list_to_matrix(input.twopt = mrk.pairs)
    plot(mat)
    ## Matrix subset
    id <- make_seq_mappoly(hexafake, 1:10)
    mat.sub <- make_mat_mappoly(mat, id)
    plot(mat.sub)