onemap (version 3.0.0)

est_map_hmm_out: C++ routine for multipoint analysis in outcrossing populations

Description

It calls C++ routine that implements the methodology of Hidden Markov Models (HMM) to construct multipoint linkage maps in outcrossing species

Usage

est_map_hmm_out(
  geno,
  error,
  type,
  phase,
  rf.vec = NULL,
  verbose = TRUE,
  tol = 1e-06
)

Value

a list containing the re-estimated vector of recombination fractions and the logarithm of the likelihood

Arguments

geno

matrix of genotypes. Rows represent marker and columns represent individuals.

type

a vector indicating the type of marker. For more information see read_onemap

phase

a vector indicating the linkage phases between markers. For more information see make_seq

rf.vec

a vector containing the recombination fraction initial values

verbose

If TRUE, print tracing information.

tol

tolerance for the C routine, i.e., the value used to evaluate convergence.