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      <img src="" class="logo" alt=""><h1>Create an SpaCET object from 10X Visium</h1>
      <small class="dont-index">Source: <a href="https://github.com/data2intelligence/SpaCET/blob/HEAD/R/utilities.R" class="external-link"><code>R/utilities.R</code></a></small>
      <div class="d-none name"><code>create.SpaCET.object.10X.Rd</code></div>
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    <div class="ref-description section level2">
    <p>Read an ST dataset to create an SpaCET object.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">create.SpaCET.object.10X</span><span class="op">(</span><span class="va">visiumPath</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
    <dl><dt>visiumPath</dt>
<dd><p>Path to the Space Ranger output folder. See ‘details’ for more information.</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    

<p>An SpaCET object.</p>
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>If users are analyzing an ST data set from 10X Visium platform, they only need to input "visiumPath".
Please make sure that "visiumPath" points to the standard output folder of 10X Space Ranger,
which have both `filtered_feature_bc_matrix` and `spatial` folders.</p>
<p>The "filtered_feature_bc_matrix" folder includes <br>
"barcodes.tsv.gz": spot level barcodes; <br>
"features.tsv.gz": list of genes; <br>
"matrix.mtx.gz": (sparse) matrix of counts.</p>
<p>The "spatial" folder includes <br>
“tissue_positions_list.csv” : barcodes and spatial information; <br>
“tissue_lowres_image.png” : hematoxylin and eosin (H&amp;E) image; <br>
“scalefactors_json.json” : scaling factors for adjusting the coordinates.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">visiumPath</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><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>package <span class="op">=</span> <span class="st">"SpaCET"</span><span class="op">)</span>, <span class="st">"extdata/Visium_BC"</span><span class="op">)</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu">create.SpaCET.object.10X</span><span class="op">(</span>visiumPath <span class="op">=</span> <span class="va">visiumPath</span><span class="op">)</span></span>
<span></span></code></pre></div>
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