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One can specify the number of permutations which corresponds to the number of TAI or TDI profiles
that are being returned as data matrix. The function then returns a TAI or TDI matrix holding
the TAI or TDI profiles of the permutated PhyloExpressionSets or DivergenceExpressionSets. This procedure
can be used for building test statistics based on the TAI or TDI profiles."><meta property="og:description" content="This function computes the TAI for a row permutated PhyloExpressionSet or DivergenceExpressionSet.
One can specify the number of permutations which corresponds to the number of TAI or TDI profiles
that are being returned as data matrix. The function then returns a TAI or TDI matrix holding
the TAI or TDI profiles of the permutated PhyloExpressionSets or DivergenceExpressionSets. This procedure
can be used for building test statistics based on the TAI or TDI profiles."><meta property="og:image" content="https://drostlab.github.io/myTAI/logo.png"></head><body>
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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.png" class="logo" alt=""><h1>Compute a Permutation Matrix for Test Statistics</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/bootMatrix.R" class="external-link"><code>R/bootMatrix.R</code></a></small>
      <div class="d-none name"><code>bootMatrix.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>This function computes the TAI for a row permutated PhyloExpressionSet or DivergenceExpressionSet.</p>
<p>One can specify the number of permutations which corresponds to the number of <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code> profiles
that are being returned as data matrix. The function then returns a <code>TAI</code> or <code>TDI</code> matrix holding
the <code>TAI</code> or <code>TDI</code> profiles of the permutated PhyloExpressionSets or DivergenceExpressionSets. This procedure
can be used for building test statistics based on the <code>TAI</code> or <code>TDI</code> profiles.</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">bootMatrix</span><span class="op">(</span><span class="va">ExpressionSet</span>, permutations <span class="op">=</span> <span class="fl">1000</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-expressionset">ExpressionSet<a class="anchor" aria-label="anchor" href="#arg-expressionset"></a></dt>
<dd><p>a standard PhyloExpressionSet or DivergenceExpressionSet object.</p></dd>


<dt id="arg-permutations">permutations<a class="anchor" aria-label="anchor" href="#arg-permutations"></a></dt>
<dd><p>a numeric value specifying the number of permutations to be performed.</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    <p>a numeric matrix representing N randomly permuted <code>TAI</code> or <code>TDI</code> profiles.</p>
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>The sampled <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code> matrix samples the phylostratum or divergence-stratum vector of
a given PhyloExpressionSet or DivergenceExpressionSet and computes the corresponding <code>TAI</code> or <code>TDI</code> profiles
of the randomly assigned phylostrata or divergence-strata. This sampling is then performed N times, yielding N randomly sampled <code>TAI</code> or <code>TDI</code> profiles.
This random <code>TAI</code> or <code>TDI</code> profile matrix can then be used to perform statistical tests
(such as the <code><a href="FlatLineTest.html">FlatLineTest</a></code>, <code><a href="ReductiveHourglassTest.html">ReductiveHourglassTest</a></code>, or <code><a href="EarlyConservationTest.html">EarlyConservationTest</a></code>) based on the significance of <code>TAI</code> or <code>TDI</code> patterns.</p>
    </div>
    <div class="section level2">
    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
    <p>Quint M et al. (2012). <em>A transcriptomic hourglass in plant embryogenesis</em>. Nature (490):  98-101.</p>
<p>Drost HG et al. (2015) Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012</p>
    </div>
    <div class="section level2">
    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
    <div class="dont-index"><p><code><a href="FlatLineTest.html">FlatLineTest</a></code>, <code><a href="ReductiveHourglassTest.html">ReductiveHourglassTest</a></code>, <code><a href="EarlyConservationTest.html">EarlyConservationTest</a></code></p></div>
    </div>
    <div class="section level2">
    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
    <p>Hajk-Georg Drost</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></span>
<span class="r-in"><span><span class="co"># read standard phylotranscriptomics data</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="va">PhyloExpressionSetExample</span><span class="op">)</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="va">DivergenceExpressionSetExample</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># example PhyloExpressionSet using 100 permutations</span></span></span>
<span class="r-in"><span><span class="va">randomTAI.Matrix</span> <span class="op">&lt;-</span> <span class="fu">bootMatrix</span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span>, permutations <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Number of Eigen threads that are employed on your machine: 12 ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Computing age assignment permutations for test statistic ... ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 
[=========================================] 100%   </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Computing variances of permuted transcriptome signatures ... ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># example DivergenceExpressionSet using 100 permutations</span></span></span>
<span class="r-in"><span><span class="va">randomTDI.Matrix</span> <span class="op">&lt;-</span> <span class="fu">bootMatrix</span><span class="op">(</span><span class="va">DivergenceExpressionSetExample</span>, permutations <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Number of Eigen threads that are employed on your machine: 12 ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Computing age assignment permutations for test statistic ... ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 
[=========================================] 100%   </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [ Computing variances of permuted transcriptome signatures ... ]</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
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