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transcriptome evolutionary index (TEI) values combined into strata"><meta property="og:description" content="computes the partial
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      <img src="../logo.png" class="logo" alt=""><h1>rcpp_pStrata_parallel</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/RcppExports.R" class="external-link"><code>R/RcppExports.R</code></a></small>
      <div class="d-none name"><code>rcpp_pStrata_parallel.Rd</code></div>
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    <div class="ref-description section level2">
    <p>computes the partial
transcriptome evolutionary index (TEI) values combined into strata</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">rcpp_pStrata_parallel</span><span class="op">(</span><span class="va">expression</span>, <span class="va">ps</span>, <span class="va">psgroup</span>, ncores <span class="op">=</span> <span class="fl">1L</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 id="arg-expression">expression<a class="anchor" aria-label="anchor" href="#arg-expression"></a></dt>
<dd><p>ExpressionSet as sparseMatrix</p></dd>


<dt id="arg-ps">ps<a class="anchor" aria-label="anchor" href="#arg-ps"></a></dt>
<dd><p>named Phylostratum</p></dd>


<dt id="arg-psgroup">psgroup<a class="anchor" aria-label="anchor" href="#arg-psgroup"></a></dt>
<dd><p>ordered unique Phylostratum</p></dd>


<dt id="arg-ncores">ncores<a class="anchor" aria-label="anchor" href="#arg-ncores"></a></dt>
<dd><p>number of cores</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    <p>sparseMatrix</p>
    </div>
    <div class="section level2">
    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
    <p>Kristian K Ullrich</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 class="r-in"><span><span class="co">## load example PhyloExpressionSetExample</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"PhyloExpressionSetExample"</span>, package<span class="op">=</span><span class="st">"myTAI"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## convert into sparseMatrix - rownames GeneID</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">spmat</span> <span class="op">&lt;-</span> <span class="fu">as</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.matrix.html" class="external-link">data.matrix</a></span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span><span class="op">[</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="fl">1</span>,<span class="fl">2</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    <span class="st">"sparseMatrix"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">spmat</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">PhyloExpressionSetExample</span><span class="op">$</span><span class="va">GeneID</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co">## create named Phylostratum vector</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ps</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/setNames.html" class="external-link">setNames</a></span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span><span class="op">$</span><span class="va">Phylostratum</span>,</span></span>
<span class="r-in"><span>    <span class="va">PhyloExpressionSetExample</span><span class="op">$</span><span class="va">GeneID</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">psgroup</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sort.html" class="external-link">sort</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unique.html" class="external-link">unique</a></span><span class="op">(</span><span class="va">ps</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">## get pStrata</span></span></span>
<span class="r-in"><span><span class="fu">rcpp_pStrata_parallel</span><span class="op">(</span><span class="va">spmat</span>, <span class="va">ps</span>, <span class="va">psgroup</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             [,1]       [,2]       [,3]       [,4]       [,5]       [,6]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] 0.39295331 0.39353082 0.41421061 0.41153988 0.42168061 0.41783018</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] 0.55914875 0.56125250 0.56064163 0.55594427 0.54154068 0.51070341</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] 0.09817938 0.09291830 0.08275821 0.08814585 0.09169432 0.09019669</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] 0.33590159 0.33335787 0.32614435 0.33717297 0.33268496 0.34456426</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] 0.16656429 0.16792339 0.15234382 0.15726786 0.15927610 0.18987539</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] 0.25872990 0.26813378 0.24458170 0.24677547 0.25514358 0.26917571</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] 0.06513175 0.05682826 0.05105236 0.05618130 0.05530130 0.05528356</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] 0.06511643 0.06180498 0.05601089 0.05588683 0.05442226 0.07020109</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] 0.09219381 0.09370185 0.09456557 0.08935340 0.07978112 0.09354879</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] 0.38766762 0.40666192 0.36664326 0.33649918 0.31130963 0.33833215</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11,] 0.06843326 0.07179705 0.06151227 0.06330899 0.06232254 0.06249801</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [12,] 0.73992167 0.71770319 0.69667019 0.71861745 0.70883635 0.73430205</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             [,7]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] 0.38838151</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] 0.47780681</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] 0.10601483</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] 0.39341385</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] 0.21135880</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] 0.34374736</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] 0.07450933</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] 0.08259620</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] 0.10997873</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] 0.32646984</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11,] 0.08185437</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [12,] 0.79420194</span>
</code></pre></div>
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