est_map_hmm_out

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

geno

a vector indicating the type of marker. For more
information see <code><a rd-options="onemap" href="/link/read_onemap?package=onemap&version=2.1.1&to=onemap" data-mini-rdoc="onemap::read_onemap">read_onemap</a></code>

type

a vector indicating the linkage phases between
markers. For more information see
<code><a rd-options="onemap" href="/link/make_seq?package=onemap&version=2.1.1&to=onemap" data-mini-rdoc="onemap::make_seq">make_seq</a></code>

phase

a vector containing the recombination fraction
initial values

rf.vec

If <code>TRUE</code>, print tracing information.

verbose

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

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

internal

Analysis of molecular marker data from model (backcrosses,
F2 and recombinant inbred lines) and non-model systems (i. e.
outcrossing species). For the later, it allows statistical
analysis by simultaneously estimating linkage and linkage
phases (genetic map construction) according to Wu et al. (2002)
<doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint
approaches using hidden Markov models.

Cristiane Taniguti

onemap

Construction of Genetic Maps in Experimental Crosses: Full-Sib,
RILs, F2 and Backcrosses

Gabriel Margarido

Marcelo Mollinari

Karl Broman

Rodrigo Amadeu

Augusto Garcia

est_map_hmm_out function

a vector indicating the type of marker. For more
information see <code><a rd-options='onemap' href='read_onemap'>read_onemap</a></code>

a vector indicating the linkage phases between
markers. For more information see
<code><a rd-options='onemap' href='make_seq'>make_seq</a></code>

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

Description

Usage

Arguments

Value