make_mat_mappoly: Subset recombination fraction matrices

In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

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)

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

Value

an object of class mappoly.rf.matrix, which is a subset of 'input.mat'. See rf_list_to_matrix 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_. \Sexpr[results=rd]{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)
   

mmollina/MAPPoly documentation built on March 8, 2024, 2:04 a.m.