est_pairwise_rf2 {mappoly}

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
)

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

Details

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

Value

An object of class mappoly.twopt2

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_. 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)