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    <h1>Sort dNdS Values Into Divergence Strata</h1>
    <small class="dont-index">Source: <a href='https://github.com/HajkD/orthologr/blob/master/R/DivergenceMap.R'><code>R/DivergenceMap.R</code></a></small>
    <div class="hidden name"><code>DivergenceMap.Rd</code></div>
    </div>

    <div class="ref-description">
    
    <p>This function takes a data.table returned by dNdS
and sorts the corresponding dNdS value into divergence strata (deciles).</p>
    
    </div>

    <pre class="usage"><span class='fu'>DivergenceMap</span>(<span class='no'>dNdS_tbl</span>, <span class='kw'>subject.id</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
    
    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>dNdS_tbl</th>
      <td><p>a data.table object returned by <code><a href='dNdS.html'>dNdS</a></code>.</p></td>
    </tr>
    <tr>
      <th>subject.id</th>
      <td><p>a logical value indicating whether <code>query_id</code> AND <code>subject_id</code> should be returned.</p></td>
    </tr>
    </table>
    
    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>a data.table storing a standard divergence map.</p>
    
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>Divergence Strata are decile values of corresponding <code><a href='dNdS.html'>dNdS</a></code> values.
The <code><a href='dNdS.html'>dNdS</a></code> function returns dNdS values for orthologous genes
of a query species (versus subject species). These dNdS values are then
sorted into deciles and each orthologous protein coding gene of the
query species receives a corresponding decile value instead of the initial dNdS value.</p>
<p>This allows a better comparison between Phylostrata and Divergence Strata (for more details see package: <span class="pkg">myTAI</span>).</p>
    
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p><code><a href='divergence_stratigraphy.html'>divergence_stratigraphy</a></code></p></div>
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># get a divergence map of example sequences</span>
<span class='no'>dNdS_tbl</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='dNdS.html'>dNdS</a></span>(
              <span class='kw'>query_file</span>      <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>'seqs/ortho_thal_cds.fasta'</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>'orthologr'</span>),
              <span class='kw'>subject_file</span>    <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>'seqs/ortho_lyra_cds.fasta'</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>'orthologr'</span>),
              <span class='kw'>ortho_detection</span> <span class='kw'>=</span> <span class='st'>"RBH"</span>,
              <span class='kw'>aa_aln_type</span>     <span class='kw'>=</span> <span class='st'>"pairwise"</span>,
              <span class='kw'>aa_aln_tool</span>     <span class='kw'>=</span> <span class='st'>"NW"</span>,
              <span class='kw'>codon_aln_tool</span>  <span class='kw'>=</span> <span class='st'>"pal2nal"</span>,
              <span class='kw'>dnds_est.method</span> <span class='kw'>=</span> <span class='st'>"Comeron"</span>,
              <span class='kw'>comp_cores</span>      <span class='kw'>=</span> <span class='fl'>1</span> )

<span class='no'>divMap</span> <span class='kw'>&lt;-</span> <span class='fu'>DivergenceMap</span>( <span class='no'>dNdS_tbl</span> )

<span class='co'># in case you want the subject_id as well, you can set</span>
<span class='co'># the argument subject.id = TRUE</span>
<span class='no'>divMap</span> <span class='kw'>&lt;-</span> <span class='fu'>DivergenceMap</span>( <span class='kw'>dNdS_tbl</span> <span class='kw'>=</span> <span class='no'>dNdS_tbl</span>, <span class='kw'>subject.id</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)

<span class='co'># }</span></pre>
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  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#arguments">Arguments</a></li>
      
      <li><a href="#value">Value</a></li>

      <li><a href="#details">Details</a></li>

      <li><a href="#see-also">See also</a></li>
      
      <li><a href="#examples">Examples</a></li>
    </ul>

    <h2>Author</h2>
    <p>Hajk-Georg Drost</p>
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