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or TDI pattern.
The reductive early conservation test is a permutation test based on the following test statistic.
- A set of developmental stages is partitioned into three modules - early, mid, and late - based on prior biological knowledge.
- The mean TAI or TDI value for each of the three modules T_early, T_mid, and T_late are computed.
- The two differences D1 = T_mid - T_early and D2 = T_late - T_early are calculated.
- The minimum D_min of D1 and D2 is computed as final test statistic of the reductive early conservation test.
This function ecScore computes the D_min value for a given TAI or TDI
stored in the age_vals argument."><meta property="og:description" content="This function computes the EarlyConservationTest score for a given TAI
or TDI pattern.
The reductive early conservation test is a permutation test based on the following test statistic.
- A set of developmental stages is partitioned into three modules - early, mid, and late - based on prior biological knowledge.
- The mean TAI or TDI value for each of the three modules T_early, T_mid, and T_late are computed.
- The two differences D1 = T_mid - T_early and D2 = T_late - T_early are calculated.
- The minimum D_min of D1 and D2 is computed as final test statistic of the reductive early conservation test.
This function ecScore computes the D_min value for a given TAI or TDI
stored in the age_vals argument."><meta property="og:image" content="https://drostlab.github.io/myTAI/logo.png"></head><body>
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      <img src="../logo.png" class="logo" alt=""><h1>Compute the Hourglass Score for the EarlyConservationTest</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/ecScore.R" class="external-link"><code>R/ecScore.R</code></a></small>
      <div class="d-none name"><code>ecScore.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>This function computes the EarlyConservationTest score for a given <code><a href="TAI.html">TAI</a></code>
or <code><a href="TDI.html">TDI</a></code> pattern.</p>
<p>The reductive early conservation test is a permutation test based on the following test statistic.</p>
<p>- A set of developmental stages is partitioned into three modules - early, mid, and late - based on prior biological knowledge.</p>
<p>- The mean <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code> value for each of the three modules T_early, T_mid, and T_late are computed.</p>
<p>- The two differences D1 = T_mid - T_early and D2 = T_late - T_early are calculated.</p>
<p>- The minimum D_min of D1 and D2 is computed as final test statistic of the reductive early conservation test.</p>
<p>This function <em>ecScore</em> computes the <em>D_min</em> value for a given <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code>
stored in the <code>age_vals</code> argument.</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">ecScore</span><span class="op">(</span><span class="va">age_vals</span>, <span class="va">early</span>, <span class="va">mid</span>, <span class="va">late</span>, profile.warn <span class="op">=</span> <span class="cn">FALSE</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-age-vals">age_vals<a class="anchor" aria-label="anchor" href="#arg-age-vals"></a></dt>
<dd><p>a numeric vector containing <code><a href="TAI.html">TAI</a></code> or <code><a href="TDI.html">TDI</a></code> values for each developmental stage s.</p></dd>


<dt id="arg-early">early<a class="anchor" aria-label="anchor" href="#arg-early"></a></dt>
<dd><p>a numeric vector storing the numeric stage values that correspond to the early phase of development.</p></dd>


<dt id="arg-mid">mid<a class="anchor" aria-label="anchor" href="#arg-mid"></a></dt>
<dd><p>a numeric vector storing the numeric stage values that correspond to the middle phase of development.</p></dd>


<dt id="arg-late">late<a class="anchor" aria-label="anchor" href="#arg-late"></a></dt>
<dd><p>a numeric vector storing the numeric stage values that correspond to the late phase of development.</p></dd>


<dt id="arg-profile-warn">profile.warn<a class="anchor" aria-label="anchor" href="#arg-profile-warn"></a></dt>
<dd><p>a boolean value indicating whether a warning is printed when a low-mid-high pattern isn't followed.</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 value representing the early conservation score.</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="EarlyConservationTest.html">EarlyConservationTest</a></code>, <code><a href="TAI.html">TAI</a></code>, <code><a href="TDI.html">TDI</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:</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># compute the TAI profile</span></span></span>
<span class="r-in"><span> <span class="va">TAIs</span> <span class="op">&lt;-</span> <span class="fu"><a href="TAI.html">TAI</a></span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># compute the early conservation score for the TAI profile</span></span></span>
<span class="r-in"><span> <span class="va">ec_score</span> <span class="op">&lt;-</span> <span class="fu">ecScore</span><span class="op">(</span>age_vals <span class="op">=</span> <span class="va">TAIs</span>,early <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>,mid <span class="op">=</span> <span class="fl">3</span><span class="op">:</span><span class="fl">5</span>,late <span class="op">=</span> <span class="fl">6</span><span class="op">:</span><span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># Example DivergenceExpressionSet:</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># compute the TDI profile</span></span></span>
<span class="r-in"><span> <span class="va">TDIs</span> <span class="op">&lt;-</span> <span class="fu"><a href="TDI.html">TDI</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"># compute the early conservation score for the TDI profile</span></span></span>
<span class="r-in"><span> <span class="va">ec_score</span> <span class="op">&lt;-</span> <span class="fu">ecScore</span><span class="op">(</span>age_vals <span class="op">=</span> <span class="va">TDIs</span>,early <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>,mid <span class="op">=</span> <span class="fl">3</span><span class="op">:</span><span class="fl">5</span>,late <span class="op">=</span> <span class="fl">6</span><span class="op">:</span><span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># compute ecScore() vector from bootMatrix()</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/apply.html" class="external-link">apply</a></span><span class="op">(</span><span class="fu"><a href="bootMatrix.html">bootMatrix</a></span><span class="op">(</span><span class="va">PhyloExpressionSetExample</span>,<span class="fl">10</span><span class="op">)</span>,<span class="fl">1</span>,<span class="va">ecScore</span>,early <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>,mid <span class="op">=</span> <span class="fl">3</span><span class="op">:</span><span class="fl">5</span>,late <span class="op">=</span> <span class="fl">6</span><span class="op">:</span><span class="fl">7</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-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> -0.05681366 -0.02292928 -0.05911419 -0.04578738 -0.02225435 -0.02986441 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>           7           8           9          10 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  0.01308162 -0.03649770  0.04031555 -0.04323258 </span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># get warning if the expected pattern isn't followed</span></span></span>
<span class="r-in"><span> <span class="va">ec_score</span> <span class="op">&lt;-</span> <span class="fu">ecScore</span><span class="op">(</span>age_vals <span class="op">=</span> <span class="va">TAIs</span>,early <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>,mid <span class="op">=</span> <span class="fl">3</span><span class="op">:</span><span class="fl">5</span>,late <span class="op">=</span> <span class="fl">6</span><span class="op">:</span><span class="fl">7</span>,profile.warn<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> The phylotranscriptomic pattern may not follow an early conservation pattern (low-mid-high or low-high-high).</span>
<span class="r-in"><span> </span></span>
</code></pre></div>
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