est_hmm_out

geno_R

error_R

type_R

phase_R

rf_R

logical to display or not the procedure

verbose_R

tol_R

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

Gabriel Margarido

Marcelo Mollinari

Getulio Ferreira

Rodrigo Amadeu

Karl Broman

Katharine Preedy

Bastian Schiffthaler

Augusto Garcia

est_hmm_out function

<dl><dt>geno_R</dt>
<dd>genotypes</dd>
<dt>error_R</dt>
<dd>genotypes probabilities</dd>
<dt>type_R</dt>
<dd>marker types</dd>
<dt>phase_R</dt>
<dd>phase estimated by 2-pts</dd>
<dt>rf_R</dt>
<dd>recombination fraction</dd>
<dt>verbose_R</dt>
<dd>logical to display or not the procedure</dd>
<dt>tol_R</dt>
<dd>EM algorithm tolerance</dd></dl>

Arguments

Run HMM chains — est_hmm_out

<dl>

<dt>geno_R</dt>
<dd>genotypes</dd>


<dt>error_R</dt>
<dd>genotypes probabilities</dd>


<dt>type_R</dt>
<dd>marker types</dd>


<dt>phase_R</dt>
<dd>phase estimated by 2-pts</dd>


<dt>rf_R</dt>
<dd>recombination fraction</dd>


<dt>verbose_R</dt>
<dd>logical to display or not the procedure</dd>


<dt>tol_R</dt>
<dd>EM algorithm tolerance</dd>

</dl>

Run HMM chains

est_hmm_out: Run HMM chains

Description

Usage

Value

Arguments