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  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Extract sample level meta.data</h1>
    <small class="dont-index">Source: <a href="https://github.com/samuel-marsh/scCustomize/blob/HEAD/R/Object_Utilities.R" class="external-link"><code>R/Object_Utilities.R</code></a></small>
    <div class="hidden name"><code>Extract_Sample_Meta.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Returns a by identity meta.data data.frame with one row per sample.  Useful for downstream
quick view of sample breakdown, meta data table creation, and/or use in pseudobulk analysis</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">Extract_Sample_Meta</span><span class="op">(</span></span>
<span>  <span class="va">object</span>,</span>
<span>  sample_name <span class="op">=</span> <span class="st">"orig.ident"</span>,</span>
<span>  variables_include <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  variables_exclude <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  include_all <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>object</dt>
<dd><p>Seurat object</p></dd>


<dt>sample_name</dt>
<dd><p>meta.data column to use as sample.  Output data.frame will contain one row per
level or unique value in this variable.</p></dd>


<dt>variables_include</dt>
<dd><p><code>@meta.data</code> columns to keep in final data.frame.  All other columns will
be discarded.  Default is NULL.</p></dd>


<dt>variables_exclude</dt>
<dd><p>columns to discard in final data.frame.  Many cell level columns are
irrelevant at the sample level (e.g., nFeature_RNA, percent_mito).</p><ul><li><p>Default parameter value is <code>NULL</code> but internally will set to discard nFeature_ASSAY(s),
nCount_ASSAY(s), percent_mito, percent_ribo, percent_mito_ribo, and log10GenesPerUMI.</p></li>
<li><p>If sample level median values are desired for these type of variables the output of this
function can be joined with output of <code><a href="Median_Stats.html">Median_Stats</a></code>.</p></li>
<li><p>Set parameter to <code>include_all = TRUE</code> to prevent any columns from being excluded.</p></li>
</ul></dd>


<dt>include_all</dt>
<dd><p>logical, whether or not to include all object meta data columns in output data.frame.
Default is FALSE.</p></dd>

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

<p>Returns a data.frame with one row per <code>sample_name</code>.</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"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://satijalab.org/seurat" class="external-link">Seurat</a></span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">pbmc_small</span><span class="op">[[</span><span class="st">"batch"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"batch1"</span>, <span class="st">"batch2"</span><span class="op">)</span>, size <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">ncol</a></span><span class="op">(</span><span class="va">pbmc_small</span><span class="op">)</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sample_meta</span> <span class="op">&lt;-</span> <span class="fu">Extract_Sample_Meta</span><span class="op">(</span>object <span class="op">=</span> <span class="va">pbmc_small</span>, sample_name <span class="op">=</span> <span class="st">"orig.ident"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Only return specific columns from meta data (orig.ident and batch)</span></span></span>
<span class="r-in"><span><span class="va">sample_meta2</span> <span class="op">&lt;-</span> <span class="fu">Extract_Sample_Meta</span><span class="op">(</span>object <span class="op">=</span> <span class="va">pbmc_small</span>, sample_name <span class="op">=</span> <span class="st">"orig.ident"</span>,</span></span>
<span class="r-in"><span>variables_include <span class="op">=</span> <span class="st">"batch"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Return all columns from meta data</span></span></span>
<span class="r-in"><span><span class="va">sample_meta3</span> <span class="op">&lt;-</span> <span class="fu">Extract_Sample_Meta</span><span class="op">(</span>object <span class="op">=</span> <span class="va">pbmc_small</span>, sample_name <span class="op">=</span> <span class="st">"orig.ident"</span>,</span></span>
<span class="r-in"><span>include_all <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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