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

In bschiffthaler/BatchMap: Software for the Creation of High Density Linkage Maps in Outcrossing Species

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

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.

Value

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

bschiffthaler/BatchMap documentation built on Dec. 16, 2019, 2:22 a.m.