mappoly (version 0.4.1)

est_pairwise_rf2: Pairwise two-point analysis - RcppParallel version

Description

Performs the two-point pairwise analysis between all markers in a sequence. For each pair, the function estimates the recombination fraction for all possible linkage phase configurations and associated LOD Scores.

Usage

est_pairwise_rf2(
  input.seq,
  ncpus = 1L,
  mrk.pairs = NULL,
  verbose = TRUE,
  tol = .Machine$double.eps^0.25
)

Value

An object of class mappoly.twopt2

Arguments

input.seq

an object of class mappoly.sequence

ncpus

Number of parallel processes (cores) to spawn (default = 1)

mrk.pairs

a matrix of dimensions 2*N, containing N pairs of markers to be analyzed. If NULL (default), all pairs are considered

verbose

If TRUE (default), current progress is shown; if FALSE, no output is produced

tol

the desired accuracy. See optimize() for details

Author

Marcelo Mollinari,

Details

Differently from est_pairwise_rf this function returns only the values associated to the best linkage phase configuration.

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

  ## Tetraploid example  
  all.mrk <- make_seq_mappoly(tetra.solcap, 100:200)
  all.pairs <- est_pairwise_rf2(input.seq = all.mrk, ncpus = 2)
  m <- rf_list_to_matrix(all.pairs)
  plot(m, fact = 2)