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filters the output by the following criteria:
1) all dN values having an NA value are omitted
2) all dS values having an NA value are omitted
3) all dNdS values &amp;gt;= the specified dnds.threshold are omitted"><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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    <h1>Filter dNdS values</h1>
    <small class="dont-index">Source: <a href="https://github.com/drostlab/orthologr/blob/HEAD/R/filter_dNdS.R" class="external-link"><code>R/filter_dNdS.R</code></a></small>
    <div class="hidden name"><code>filter_dNdS.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function takes the output data.table returned by <code><a href="dNdS.html">dNdS</a></code> and
filters the output by the following criteria:</p>
<p>1) all dN values having an NA value are omitted</p>
<p>2) all dS values having an NA value are omitted</p>
<p>3) all dNdS values &gt;= the specified <code>dnds.threshold</code> are omitted</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">filter_dNdS</span><span class="op">(</span><span class="va">dNdS_tbl</span>, dnds.threshold <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>dNdS_tbl</dt>
<dd><p>a <code>data.table</code> returned by <code><a href="dNdS.html">dNdS</a></code>.</p></dd>


<dt>dnds.threshold</dt>
<dd><p>a numeric value specifying the dnds threshold for genes that shall be retained.
Hence all genes having a dNdS value &lt;= <code>dnds.threshold</code> are retained. Default is <code>dnds.threshold</code> = 2.</p></dd>

</dl></div>
    <div id="details">
    <h2>Details</h2>
    <p>The dNdS ratio quantifies the selection pressure acting on a given protein sequence.</p>
<p>It is proposed that:</p>
<p>1) dNdS values &lt; 1 reflect stabilizing selection of a protein</p> 
<p>2) dNdS value = 1 reflect neutral selection of a protein</p> 
<p>3) dNdS values &gt; 1 reflect variational selection of a protein</p>
<p>Now an assumption must be generated to allow for dNdS filtering.
Given a <code>dnds.threshold</code> all value above this threshold are omitted from the dataset.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="dNdS.html">dNdS</a></code>, <code><a href="divergence_stratigraphy.html">divergence_stratigraphy</a></code></p></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Hajk-Georg Drost</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">filter_dNdS</span><span class="op">(</span> <span class="fu"><a href="dNdS.html">dNdS</a></span><span class="op">(</span> query_file <span class="op">=</span> </span></span>
<span class="r-in"><span>                   <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>                   subject_file <span class="op">=</span> </span></span>
<span class="r-in"><span>                   <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>                   ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>                   aa_aln_type <span class="op">=</span> <span class="st">"pairwise"</span>,</span></span>
<span class="r-in"><span>                   aa_aln_tool <span class="op">=</span> <span class="st">"NW"</span>,</span></span>
<span class="r-in"><span>                   codon_aln_tool <span class="op">=</span> <span class="st">"pal2nal"</span>, </span></span>
<span class="r-in"><span>                   dnds_est.method <span class="op">=</span> <span class="st">"Comeron"</span>, </span></span>
<span class="r-in"><span>                   comp_cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, </span></span>
<span class="r-in"><span>             dnds.threshold <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># a small example using clustalw</span></span></span>
<span class="r-in"><span><span class="fu">filter_dNdS</span><span class="op">(</span> <span class="fu"><a href="dNdS.html">dNdS</a></span><span class="op">(</span> query_file      <span class="op">=</span> </span></span>
<span class="r-in"><span>                   <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>                   subject_file    <span class="op">=</span> </span></span>
<span class="r-in"><span>                   <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>                   ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>                   aa_aln_type     <span class="op">=</span> <span class="st">"pairwise"</span>,</span></span>
<span class="r-in"><span>                   aa_aln_tool     <span class="op">=</span> <span class="st">"NW"</span>,</span></span>
<span class="r-in"><span>                   codon_aln_tool  <span class="op">=</span> <span class="st">"pal2nal"</span>, </span></span>
<span class="r-in"><span>                   dnds_est.method <span class="op">=</span> <span class="st">"Comeron"</span>, </span></span>
<span class="r-in"><span>                   comp_cores      <span class="op">=</span> <span class="fl">1</span><span class="op">)</span> , </span></span>
<span class="r-in"><span>               dnds.threshold  <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
<span class="r-in"><span>                  </span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
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