reest_rf {mappoly}

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
)

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

Value

An updated object of class mappoly.pcmap whose order was used in the input.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_. 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 doi:10.1111/j.1365-313X.1993.00739.x