mappoly (version 0.2.3)

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)

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

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_. 10.1534/g3.119.400378

Examples

# NOT RUN {
    # 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)
   
# }