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    <div class="page-header">
    <h1>Main Orthology Inference Function</h1>
    <small class="dont-index">Source: <a href="https://github.com/drostlab/orthologr/blob/HEAD/R/orthologs.R" class="external-link"><code>R/orthologs.R</code></a></small>
    <div class="hidden name"><code>orthologs.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function takes nucleotide or protein sequences for a set of organisms 
and performs orthology inference to detect orthologous genes within the given organisms
based on selected orthology inference programs.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">orthologs</span><span class="op">(</span></span>
<span>  <span class="va">query_file</span>,</span>
<span>  <span class="va">subject_files</span>,</span>
<span>  seq_type <span class="op">=</span> <span class="st">"protein"</span>,</span>
<span>  outgroup_file <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  eval <span class="op">=</span> <span class="st">"1E-5"</span>,</span>
<span>  format <span class="op">=</span> <span class="st">"fasta"</span>,</span>
<span>  ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>,</span>
<span>  delete_corrupt_cds <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  cdd.path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  add_params <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  comp_cores <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  clean_folders <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>query_file</dt>
<dd><p>a character string specifying the path to the sequence file of interest (query organism).</p></dd>


<dt>subject_files</dt>
<dd><p>a character string specifying the paths to the sequence files of interest (subject organisms).
Different orthology inference methods can detect orthologs using multiple subject organisms, e.g. "OrthoMCL", and "PO" (ProteinOrtho).</p></dd>


<dt>seq_type</dt>
<dd><p>a character string specifying the sequence type stored in the input file.
Options are are: "cds", "protein", or "dna". In case of "cds", sequence are translated to protein sequences,
in case of "dna", cds prediction is performed on the corresponding sequences which subsequently are
translated to protein sequences. Default is <code>seq_type</code> = "protein".</p></dd>


<dt>outgroup_file</dt>
<dd><p>a character string specifying the paths to the sequence files of interest (outgroup organisms).
This argument is only used by <code>InParanoid</code>.</p></dd>


<dt>eval</dt>
<dd><p>a numeric value specifying the E-Value cutoff for BLAST hit detection.</p></dd>


<dt>format</dt>
<dd><p>a character string specifying the file format of the sequence file, e.g. "fasta", "gbk". Default is "fasta".</p></dd>


<dt>ortho_detection</dt>
<dd><p>a character string specifying the orthology inference method that shall be performed
to detect orthologous genes. Default is <code>ortho_detection</code> = "RBH" (BLAST reciprocal best hit).
Further methods are: "RBH" (BLAST reciprocal best hit), "PO" (ProteinOrtho), and "OrthoMCL.</p></dd>


<dt>delete_corrupt_cds</dt>
<dd><p>a logical value indicating whether sequences with corrupt base triplets should be removed from the input <code>file</code>. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.</p></dd>


<dt>cdd.path</dt>
<dd><p>path to the cdd database folder (specify when using <code>ortho_detection</code> = <code>"DELTA"</code>).</p></dd>


<dt>path</dt>
<dd><p>a character string specifying the path to the corresponding orthology inference tool.
For "BH" and "RBH": path to BLAST, "PO": path to ProteinOrtho 5.07, "OrthoMCL": path to OrthoMCL.</p></dd>


<dt>add_params</dt>
<dd><p>a character string specifying additional parameters that shall be handed to the orthology inference method (tool).
Default is <code>add_params</code> = <code>NULL</code>.</p></dd>


<dt>comp_cores</dt>
<dd><p>a numeric value specifying the number of cores to be used for multicore computations.</p></dd>


<dt>quiet</dt>
<dd><p>a logical value specifying whether a successful interface call shall be printed out.</p></dd>


<dt>clean_folders</dt>
<dd><p>a boolean value spefiying whether all internall folders storing the output of used programs
shall be removed. Default is <code>clean_folders</code> = <code>FALSE</code>.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes
in the second column and the amino acid sequences in the third column.</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>This function takes sequence files of a query organism and a subject organism and performs orthology inference
using a defined orthology inference method to dectect orthologous genes.</p>
<p>The following interfaces are implemented in the <code>orthologs</code> function:</p> 
<p>BLAST based methods:</p>
<ul><li><p>BLAST best hit (BH)</p></li>
<li><p>BLAST reciprocal best hit (RBH)</p></li>
<li><p>DELTA-BLAST reciprocal best hit (DELTA)</p></li>
</ul></div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="blast_rec.html">blast_rec</a></code>, <code><a href="dNdS.html">dNdS</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="co">### BLAST Best Hit</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># perform orthology inference using BLAST best hit</span></span></span>
<span class="r-in"><span><span class="co"># and fasta sequence files storing protein sequences</span></span></span>
<span class="r-in"><span><span class="fu">orthologs</span><span class="op">(</span>query_file      <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          subject_files   <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          seq_type        <span class="op">=</span> <span class="st">"protein"</span>, </span></span>
<span class="r-in"><span>          ortho_detection <span class="op">=</span> <span class="st">"BH"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">### BLAST Reciprocal Best Hit</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># perform orthology inference using BLAST reciprocal best hit</span></span></span>
<span class="r-in"><span><span class="co"># and fasta sequence files storing protein sequences</span></span></span>
<span class="r-in"><span><span class="fu">orthologs</span><span class="op">(</span>query_file      <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          subject_files   <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          seq_type        <span class="op">=</span> <span class="st">"protein"</span>, </span></span>
<span class="r-in"><span>          ortho_detection <span class="op">=</span> <span class="st">"RBH"</span><span class="op">)</span></span></span>
<span class="r-in"><span>          </span></span>
<span class="r-in"><span>          </span></span>
<span class="r-in"><span><span class="co"># multicore version          </span></span></span>
<span class="r-in"><span><span class="fu">orthologs</span><span class="op">(</span>query_file      <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          subject_files   <span class="op">=</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_aa.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>          seq_type        <span class="op">=</span> <span class="st">"protein"</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>          comp_cores      <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>          </span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
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