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or TDI pattern.
The pair test is a permutation test based on the following test statistic.
- A PhyloExpressionSet is partitioned into contrast pairs - contrast1 and contrast2 - based on prior biological knowledge.
This prior knowledge could include sexual, ecological and genetic backgrounds.
- The mean TAI or TDI value for each of the two contrasts contrast1 and contrast2 are computed.
- The pairwise differences D_constrast = contrast1 - contrast2 is calculated as final test statistic of the pair test,
when the altHypothesis is specified as "greater". When the altHypothesis is specified as "less", sign of D_constrast is reversed.
This function pairScore computes the D_contrast value for a given TAI or TDI
stored in the age_vals argument.'><meta property="og:description" content='This function computes the PairwiseTest score for a given TAI
or TDI pattern.
The pair test is a permutation test based on the following test statistic.
- A PhyloExpressionSet is partitioned into contrast pairs - contrast1 and contrast2 - based on prior biological knowledge.
This prior knowledge could include sexual, ecological and genetic backgrounds.
- The mean TAI or TDI value for each of the two contrasts contrast1 and contrast2 are computed.
- The pairwise differences D_constrast = contrast1 - contrast2 is calculated as final test statistic of the pair test,
when the altHypothesis is specified as "greater". When the altHypothesis is specified as "less", sign of D_constrast is reversed.
This function pairScore computes the D_contrast 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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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.png" class="logo" alt=""><h1>Compute the Pairwise Difference in TAI Score</h1>
      <small class="dont-index">Source: <a href="https://github.com/drostlab/myTAI/blob/HEAD/R/pairScore.R" class="external-link"><code>R/pairScore.R</code></a></small>
      <div class="d-none name"><code>pairScore.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>This function computes the PairwiseTest 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 pair test is a permutation test based on the following test statistic.</p>
<p>- A PhyloExpressionSet is partitioned into contrast pairs - contrast1 and contrast2 - based on prior biological knowledge.
This prior knowledge could include sexual, ecological and genetic backgrounds.</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 two contrasts contrast1 and contrast2 are computed.</p>
<p>- The pairwise differences D_constrast = contrast1 - contrast2 is calculated as final test statistic of the pair test,
when the <code>altHypothesis</code> is specified as "greater". When the <code>altHypothesis</code> is specified as "less", sign of D_constrast is reversed.</p>
<p>This function <em>pairScore</em> computes the <em>D_contrast</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">pairScore</span><span class="op">(</span><span class="va">age_vals</span>, <span class="va">contrast1</span>, <span class="va">contrast2</span>, altHypothesis <span class="op">=</span> <span class="cn">NULL</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-contrast-">contrast1<a class="anchor" aria-label="anchor" href="#arg-contrast-"></a></dt>
<dd><p>a numeric vector storing the numeric stage values that correspond to the query contrast.</p></dd>


<dt id="arg-contrast-">contrast2<a class="anchor" aria-label="anchor" href="#arg-contrast-"></a></dt>
<dd><p>a numeric vector storing the numeric stage values that correspond to the subject contrast.</p></dd>


<dt id="arg-althypothesis">altHypothesis<a class="anchor" aria-label="anchor" href="#arg-althypothesis"></a></dt>
<dd><p>a character string defining the alternative hypothesis
used to quantify the statistical significance in the present phylotranscriptomics pattern.
Possible values can be:</p><ul><li><p><code>altHypothesis</code> = <code>"greater"</code> : contrast1 &gt; contrast2</p></li>
<li><p><code>altHypothesis</code> = <code>"less"</code> : contrast1 &lt; contrast2</p></li>
</ul></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 pair 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="PairwiseTest.html">PairwiseTest</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 and Jaruwatana Sodai Lotharukpong</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 pair score for the first two stages in the TAI profile</span></span></span>
<span class="r-in"><span> <span class="co"># we test whether TAI in contrast1 is greater than contrast 2.</span></span></span>
<span class="r-in"><span> <span class="va">pair_score</span> <span class="op">&lt;-</span> <span class="fu">pairScore</span><span class="op">(</span>age_vals <span class="op">=</span> <span class="va">TAIs</span>,contrast1 <span class="op">=</span> <span class="fl">1</span>,contrast2 <span class="op">=</span> <span class="fl">2</span>,</span></span>
<span class="r-in"><span>                         altHypothesis<span class="op">=</span><span class="st">"greater"</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 pair score for the first two stages in the TDI profile</span></span></span>
<span class="r-in"><span> <span class="co"># we test whether TDI in contrast1 is greater than contrast 2.</span></span></span>
<span class="r-in"><span> <span class="va">pair_score</span> <span class="op">&lt;-</span> <span class="fu">pairScore</span><span class="op">(</span>age_vals <span class="op">=</span> <span class="va">TDIs</span>,contrast1 <span class="op">=</span> <span class="fl">1</span>,contrast2 <span class="op">=</span> <span class="fl">2</span>,</span></span>
<span class="r-in"><span>                         altHypothesis<span class="op">=</span><span class="st">"greater"</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># compute pairScore() 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></span>
<span class="r-in"><span>       <span class="va">pairScore</span>,contrast1 <span class="op">=</span> <span class="fl">1</span>,contrast2 <span class="op">=</span> <span class="fl">2</span>, altHypothesis<span class="op">=</span><span class="st">"greater"</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 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  0.0094227374  0.0102870656 -0.0022944993 -0.0045077845 -0.0006856504 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             6             7             8             9            10 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  0.0113790720 -0.0178215366 -0.0011520399  0.0040270946 -0.0192558721 </span>
<span class="r-in"><span> </span></span>
</code></pre></div>
    </div>
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