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    <h1>Copy Number Quantification of predicted LTRs (solo LTR prediction)</h1>
    <small class="dont-index">Source: <a href='https://github.com/HajkD/LTRpred/blob/master/R/ltr.cn.R'><code>R/ltr.cn.R</code></a></small>
    <div class="hidden name"><code>ltr.cn.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Detect solo LTR copies and genomic locations of predicted LTR transposons using a BLAST search strategy.</p>
    </div>

    <pre class="usage"><span class='fu'>ltr.cn</span><span class='op'>(</span>
  <span class='va'>data.sheet</span>,
  <span class='va'>LTR.fasta_3ltr</span>,
  <span class='va'>LTR.fasta_5ltr</span>,
  <span class='va'>genome</span>,
  ltr.similarity <span class='op'>=</span> <span class='fl'>70</span>,
  scope.cutoff <span class='op'>=</span> <span class='fl'>0.85</span>,
  perc.ident.cutoff <span class='op'>=</span> <span class='fl'>70</span>,
  output <span class='op'>=</span> <span class='cn'>NULL</span>,
  max.hits <span class='op'>=</span> <span class='fl'>500</span>,
  eval <span class='op'>=</span> <span class='fl'>1e-10</span>,
  cores <span class='op'>=</span> <span class='fl'>1</span>
<span class='op'>)</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>data.sheet</th>
      <td><p>path to the <code>*_LTRpred_DataSheet.csv</code> file generated by <code><a href='LTRpred.html'>LTRpred</a></code>.</p></td>
    </tr>
    <tr>
      <th>LTR.fasta_3ltr</th>
      <td><p>path to fasta file storing sequences of 3 prime LTRs generated by <code><a href='LTRpred.html'>LTRpred</a></code>.</p></td>
    </tr>
    <tr>
      <th>LTR.fasta_5ltr</th>
      <td><p>path to fasta file storing sequences of 5 prime LTRs generated by <code><a href='LTRpred.html'>LTRpred</a></code>.</p></td>
    </tr>
    <tr>
      <th>genome</th>
      <td><p>file path to the reference genome in which solo LTRs shall be found (in <code>fasta</code> format).</p></td>
    </tr>
    <tr>
      <th>ltr.similarity</th>
      <td><p>similarity threshold for defining LTR similarity.</p></td>
    </tr>
    <tr>
      <th>scope.cutoff</th>
      <td><p>similarity threshold for the scope variable. The scope of a BLAST hit is defined by <code>abs(s_len - alig_length) / s_len</code>
and aims to quantify the scope ('length similarity between hit and query') of the alignment. Default is <code>scope.cutoff = 0.85</code> meaning that
at least 85% of the length of the query sequence must match with the length of the subject sequence.</p></td>
    </tr>
    <tr>
      <th>perc.ident.cutoff</th>
      <td><p>choose the minimum sequence identity between the query sequence and subject hit sequence that have a scope &gt;= <code>scope.cutoff</code> (e.g. 0.85). 
Default is <code>perc.ident.cutoff = 70</code>. This threshold aims to detect BLAST hits that have similar sequence lengths 
(controlled by the <code>scope.cutoff</code> variable; e.g. <code>scope.cutoff = 0.85</code>) and within this scope at least e.g. 70% sequence identity (controlled by the <code>perc.ident.cutoff</code> variable).</p></td>
    </tr>
    <tr>
      <th>output</th>
      <td><p>file name of the BLAST output. If <code>output = NULL</code> (default) then the BLAST output file will be deleted after the result <code>data.frame</code> is returned by this function.</p></td>
    </tr>
    <tr>
      <th>max.hits</th>
      <td><p>maximum number of hits that shall be retrieved that still fulfill the e-value criterium.
Default is <code>max.hits = 65000</code>.</p></td>
    </tr>
    <tr>
      <th>eval</th>
      <td><p>e-value threshold for BLAST hit detection. Default is <code>eval = 1E-10</code>.</p></td>
    </tr>
    <tr>
      <th>cores</th>
      <td><p>number of cores for parallel computations.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

    <p>Altschul, S.F., Gish, W., Miller, W., Myers, E.W. &amp; Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.</p>
<p>Gish, W. &amp; States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.</p>
<p>Madden, T.L., Tatusov, R.L. &amp; Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.</p>
<p>Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W. &amp; Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.</p>
<p>Zhang Z., Schwartz S., Wagner L., &amp; Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.</p>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Hajk-Georg Drost</p>

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