reest_rf: Re-estimate the recombination fractions in a genetic map

Description

This function re-estimates the recombination fractions between all markers in a given map.

Usage

reest_rf(
  input.map,
  input.mat = NULL,
  tol = 0.01,
  phase.config = "all",
  method = c("hmm", "ols", "wMDS_to_1D_pc"),
  weight = TRUE,
  verbose = TRUE,
  high.prec = FALSE,
  max.rf.to.break.EM = 0.5,
  input.mds = NULL
)

Value

An updated object of class mappoly.pcmap whose order was used in the input.map

Arguments

input.map: An object of class mappoly.map
input.mat: An object of class mappoly.rf.matrix
tol: tolerance for determining convergence (default = 10e-03)
phase.config: which phase configuration should be used. "best" (default) will choose the maximum likelihood configuration
method: indicates whether to use 'hmm' (Hidden Markov Models), 'ols' (Ordinary Least Squares) or 'wMDS_to_1D_pc' (weighted MDS followed by fitting a one dimensional principal curve) to re-estimate the recombination fractions.
weight: if TRUE (default), it uses the LOD scores to perform a weighted regression when the Ordinary Least Squares is chosen
verbose: if TRUE (default), current progress is shown; if FALSE, no output is produced
high.prec: logical. If TRUE uses high precision (long double) numbers in the HMM procedure implemented in C++, which can take a long time to perform (default = FALSE)
max.rf.to.break.EM: for internal use only.
input.mds: An object of class mappoly.map

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")

Stam P (1993) Construction of integrated genetic-linkage maps by means of a new computer package: Joinmap. _Plant J_ 3:739–744 tools:::Rd_expr_doi("10.1111/j.1365-313X.1993.00739.x")