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<img src="../logo.svg" class="logo" alt=""><h1>Export Data Set as NCBI BioSample Antibiogram</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/export_biosample.R" class="external-link"><code>R/export_biosample.R</code></a></small>
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<div class="d-none name"><code>export_ncbi_biosample.Rd</code></div>
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<div class="ref-description section level2">
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<p>Export Data Set as NCBI BioSample Antibiogram</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">export_ncbi_biosample</span><span class="op">(</span></span>
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<span> <span class="va">x</span>,</span>
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<span> filename <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"biosample_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"%Y-%m-%d-%H%M%S"</span><span class="op">)</span>, <span class="st">".xlsx"</span><span class="op">)</span>,</span>
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<span> type <span class="op">=</span> <span class="st">"pathogen MIC"</span>,</span>
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<span> columns <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>,</span>
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<span> save_as_xlsx <span class="op">=</span> <span class="cn">TRUE</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a data set</p></dd>
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<dt>filename</dt>
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<dd><p>a character string specifying the file name</p></dd>
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<dt>type</dt>
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<dd><p>a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <a href="https://www.ncbi.nlm.nih.gov/biosample/docs/" class="external-link">https://www.ncbi.nlm.nih.gov/biosample/docs/</a></p></dd>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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