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    <h1>Infer orthologous lncRNAs between multiple species</h1>
    <small class="dont-index">Source: <a href="https://github.com/drostlab/orthologr/blob/HEAD/R/map.generator.lnc.R" class="external-link"><code>R/map.generator.lnc.R</code></a></small>
    <div class="hidden name"><code>map_generator_lnc.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Inference of orthologous lncRNAs between multiple species is performed via pairwise BLAST (reciprocal) best hit comparisons.
 The corresponding orthologous tables are then stored in an output folder.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">map_generator_lnc</span><span class="op">(</span></span>
<span>  <span class="va">query_file</span>,</span>
<span>  <span class="va">subjects_folder</span>,</span>
<span>  <span class="va">output_folder</span>,</span>
<span>  task <span class="op">=</span> <span class="st">"blastn"</span>,</span>
<span>  eval <span class="op">=</span> <span class="st">"1E-5"</span>,</span>
<span>  ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>,</span>
<span>  max.target.seqs <span class="op">=</span> <span class="fl">10000</span>,</span>
<span>  min_qry_coverage_hsp <span class="op">=</span> <span class="fl">30</span>,</span>
<span>  min_qry_perc_identity <span class="op">=</span> <span class="fl">30</span>,</span>
<span>  logical_connective <span class="op">=</span> <span class="st">"AND"</span>,</span>
<span>  min_alig_length <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  comp_cores <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  progress_bar <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  sep <span class="op">=</span> <span class="st">";"</span>,</span>
<span>  path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  <span class="va">...</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 lncRNAs file of the query organism in <code>fasta</code> format.</p></dd>


<dt>subjects_folder</dt>
<dd><p>a character string specifying the path to the folder where lncRNAs files in <code>fasta</code> format of the subject organisms are stored.</p></dd>


<dt>output_folder</dt>
<dd><p>a character string specifying the path to the folder where output orthologous tables should be stored.</p></dd>


<dt>task</dt>
<dd><p>nucleotide search task option. Options are:</p><ul><li><p><code>task = "blastn"</code> : Standard nucleotide-nucleotide comparisons (default) - Traditional BLASTN requiring an exact match of 11.</p></li>
<li><p><code>task = "blastn-short"</code> : Optimized nucleotide-nucleotide comparisons for query sequences shorter than 50 nucleotides.</p></li>
<li><p><code>task = "dc-megablast"</code> : Discontiguous megablast used to find somewhat distant sequences.</p></li>
<li><p><code>task = "megablast"</code> : Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences.</p></li>
<li><p><code>task = "rmblastn"</code></p></li>
</ul></dd>


<dt>eval</dt>
<dd><p>a character string specifying the e-value for BLAST based orthology inference. Please use the scientific notation.</p></dd>


<dt>ortho_detection</dt>
<dd><p>a character string specifying the Orthology Inference method that shall be used to perform
dNdS computations. Possible options are:</p><ul><li><p><code>ortho_detection = "BH"</code>: BLAST best unidirectional hit</p></li>
<li><p><code>ortho_detection = "RBH"</code>: BLAST best reciprocal hit</p></li>
</ul></dd>


<dt>max.target.seqs</dt>
<dd><p>a numeric value specifying the number of aligned sequences to keep.
Please be aware that <code>max.target.seqs</code> selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 .</p></dd>


<dt>min_qry_coverage_hsp</dt>
<dd><p>minimum <code>qcovhsp</code> (= query coverage of the HSP) of an orthologous hit (a value between 1 and 100).</p></dd>


<dt>min_qry_perc_identity</dt>
<dd><p>minimum <code>perc_identity</code> (= percent sequence identity between query and selected HSP) of an orthologous hit (a value between 1 and 100).</p></dd>


<dt>logical_connective</dt>
<dd><p>character representing logical connective (either "AND" or "OR") if <code>min_alig_length</code> is not <code>NULL</code> filtering is done on <code>min_alig_length</code> and/or <code>min_qry_perc_identity</code></p></dd>


<dt>min_alig_length</dt>
<dd><p>minimum <code>alig_length</code> (alignment length) to an orthologous hit (number of aligned nucleotides or amino acids depending on the input data)</p></dd>


<dt>comp_cores</dt>
<dd><p>number of computing cores that shall be used to perform parallelized computations.</p></dd>


<dt>progress_bar</dt>
<dd><p>should a progress bar be shown. Default is <code>progress_bar = TRUE</code>.</p></dd>


<dt>sep</dt>
<dd><p>a file separator that is used to store maps as csv file.</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>...</dt>
<dd><p>additional parameters that shall be passed to  <code><a href="dNdS.html">dNdS</a></code>.</p></dd>

</dl></div>
    <div id="details">
    <h2>Details</h2>
    <p>Given a query organism and a set of subject organsisms that are stored in the same folder,
this function crawls through all subject organsism and infers the lncRNA homologs in
pairwise species comparisons.</p>
    </div>
    <div id="note">
    <h2>Note</h2>
    <p>According to Sarropoulos, I., et al. (2019) orthology detection of lncRNAs was performed by reciprocal BLAST searches. Significant hits with an e-value &lt;= 10-3 were selected having an alignment identity &gt;= 10% OR a minimum alignment length &gt;= 50 nucleotides.</p>
    </div>
    <div id="references">
    <h2>References</h2>
    <p>Sarropoulos I, Marin R, Cardoso-Moreira M, Kaessmann H (2019).
“Developmental dynamics of lncRNAs across mammalian organs and species.”
<em>Nature</em>, <b>571</b>, 510--514.</p>
    </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 class="co"># example using classic blastn searches</span></span></span>
<span class="r-in"><span><span class="fu">map_generator_lnc</span><span class="op">(</span></span></span>
<span class="r-in"><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_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   subjects_folder <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/map_gen_example'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   output_folder   <span class="op">=</span> <span class="st">"orthologs_lncrna"</span>,</span></span>
<span class="r-in"><span>   comp_cores      <span class="op">=</span> <span class="fl">1</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># example using  discontiguous megablast used to find somewhat distant sequences</span></span></span>
<span class="r-in"><span><span class="fu">map_generator_lnc</span><span class="op">(</span></span></span>
<span class="r-in"><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_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   subjects_folder <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/map_gen_example'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>   output_folder   <span class="op">=</span> <span class="st">"orthologs_lncrna"</span>,</span></span>
<span class="r-in"><span>   task            <span class="op">=</span> <span class="st">"dc-megablast"</span>,</span></span>
<span class="r-in"><span>   comp_cores      <span class="op">=</span> <span class="fl">1</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><span></span></span>
<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 class="co"># parameter settings based on Sarropoulos, I., et al. (2019)</span></span></span>
<span class="r-in"><span><span class="fu">map_generator_lnc</span><span class="op">(</span></span></span>
<span class="r-in"><span>   <span class="va">query_file</span>,,</span></span>
<span class="r-in"><span>   <span class="va">subjects_folder</span>,</span></span>
<span class="r-in"><span>   eval                  <span class="op">=</span> <span class="fl">1E-3</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>   <span class="va">output_folder</span>,</span></span>
<span class="r-in"><span>   min_qry_coverage_hsp  <span class="op">=</span> <span class="fl">0</span>,</span></span>
<span class="r-in"><span>   min_qry_perc_identity <span class="op">=</span> <span class="fl">10</span>,</span></span>
<span class="r-in"><span>   logical_connective    <span class="op">=</span> <span class="st">"OR"</span>,</span></span>
<span class="r-in"><span>   min_alig_length       <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
</code></pre></div>
    </div>
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