make_pairs_mappoly: Subset pairwise recombination fractions
In mmollina/MAPPoly: Genetic Linkage Maps in Autopolyploids

make_pairs_mappoly

R Documentation

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, mmollin@ncsu.edu

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

    ## 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")

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