RTIGER-class

.RTIGER

This class is a generic container for RTIGER analysis

Our method integrates information from all sequenced samples, thus avoiding loss of alleles due to low coverage. Moreover, it increases the statistical power to uncover sequencing or alignment errors <doi:10.1093/plphys/kiad191>.

Rafael Campos-Martin

RTIGER

HMM-Based Model for Genotyping and Cross-Over Identification

Sophia Schmickler

Manish Goel

Korbinian Schneeberger

Achim Tresch

RTIGER-class function

<dl>
<dt><code>matobs</code></dt>
<dd>Nested lists. the first level is a list of samples. For each sample there are 5 matrices that contains the allele counts for each position.</dd></dl>
<dt><code>params</code></dt>
<dd>a list with the parameters after training.</dd>
<dt><code>info</code></dt>
<dd>List with phenotipic data of the samples.</dd>
<dt><code>Viterbi</code></dt>
<dd>List of chromosomes with the viterbi path per sample.</dd>
<dt><code>Probabilities</code></dt>
<dd>Computed probabilites for the EM algorithm.</dd>
<dt><code>num.iter</code></dt>
<dd>Number of iterations needed to stop the EM algorithm.</dd>

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This class is a generic container for RTIGER analysis — RTIGER-class

<dl>
<dt><code>matobs</code></dt>
<dd>Nested lists. the first level is a list of samples. For each sample there are 5 matrices that contains the allele counts for each position.</dd>


<dt><code>params</code></dt>
<dd>a list with the parameters after training.</dd>


<dt><code>info</code></dt>
<dd>List with phenotipic data of the samples.</dd>


<dt><code>Viterbi</code></dt>
<dd>List of chromosomes with the viterbi path per sample.</dd>


<dt><code>Probabilities</code></dt>
<dd>Computed probabilites for the EM algorithm.</dd>


<dt><code>num.iter</code></dt>
<dd>Number of iterations needed to stop the EM algorithm.</dd>


</dl>

RTIGER-class: This class is a generic container for RTIGER analysis

Description

Arguments

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