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+<meta property="og:description" content="Performs variance shrinkage via application of an empirical Bayes procedure
+(of LIMMA) on the observed data after a transformation moving the data to
+influence function space, based on the average treatment effect parameter." />
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Moderated Statistical Tests for Influence Functions</h1>
+    <small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/eif_moderated.R'><code>R/eif_moderated.R</code></a></small>
+    <div class="hidden name"><code>modtest_ic.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Performs variance shrinkage via application of an empirical Bayes procedure
+(of LIMMA) on the observed data after a transformation moving the data to
+influence function space, based on the average treatment effect parameter.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>modtest_ic</span><span class='op'>(</span><span class='va'>biotmle</span>, adjust <span class='op'>=</span> <span class='st'>"BH"</span>, pval_type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"normal"</span>, <span class='st'>"logistic"</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>biotmle</th>
+      <td><p><code>biotmle</code> object as generated by <code>biomarkertmle</code></p></td>
+    </tr>
+    <tr>
+      <th>adjust</th>
+      <td><p>the multiple testing correction to be applied to p-values that
+are generated from the moderated tests. The recommended (default) method
+is that of Benjamini and Hochberg. See <a href='https://rdrr.io/pkg/limma/man/toptable.html'>topTable</a> for a list of
+appropriate methods.</p></td>
+    </tr>
+    <tr>
+      <th>pval_type</th>
+      <td><p>The reference distribution to be used for computing the
+p-value. Those based on the normal approximation tend to provide misleading
+inference when working with moderately sized (finite) samples. Use of the
+logistic distribution has been found to empirically improve performance in
+settings where multiple hypothesis testing is a concern.</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Other arguments passed to <code><a href='https://rdrr.io/pkg/limma/man/toptable.html'>topTable</a></code>.</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p><code>biotmle</code> object containing the results of applying both
+ <code><a href='https://rdrr.io/pkg/limma/man/lmFit.html'>lmFit</a></code> and <code><a href='https://rdrr.io/pkg/limma/man/toptable.html'>topTable</a></code>.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://dplyr.tidyverse.org'>dplyr</a></span><span class='op'>)</span>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>biotmleData</span><span class='op'>)</span>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://github.com/ecpolley/SuperLearner'>SuperLearner</a></span><span class='op'>)</span>
+<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://bioconductor.org/packages/SummarizedExperiment'>SummarizedExperiment</a></span><span class='op'>)</span>
+<span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span>
+
+<span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+  <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+  <span class='fu'>dplyr</span><span class='fu'>::</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>age <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/numeric.html'>as.numeric</a></span><span class='op'>(</span><span class='va'>age</span> <span class='op'>&gt;</span> <span class='fu'><a href='https://rdrr.io/r/stats/median.html'>median</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
+  <span class='fu'>DataFrame</span><span class='op'>(</span><span class='op'>)</span>
+<span class='va'>benz_idx</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>colData</a></span><span class='op'>(</span><span class='va'>illuminaData</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%in%</span> <span class='st'>"benzene"</span><span class='op'>)</span>
+
+<span class='va'>biomarkerTMLEout</span> <span class='op'>&lt;-</span> <span class='fu'><a href='biomarkertmle.html'>biomarkertmle</a></span><span class='op'>(</span>
+  se <span class='op'>=</span> <span class='va'>illuminaData</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>, <span class='op'>]</span>,
+  varInt <span class='op'>=</span> <span class='va'>benz_idx</span>,
+  bppar_type <span class='op'>=</span> <span class='fu'>BiocParallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/BiocParallel/man/SerialParam-class.html'>SerialParam</a></span><span class='op'>(</span><span class='op'>)</span>,
+  g_lib <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SL.mean"</span>, <span class='st'>"SL.glm"</span><span class='op'>)</span>,
+  Q_lib <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SL.mean"</span>, <span class='st'>"SL.glm"</span><span class='op'>)</span>
+<span class='op'>)</span>
+</div><div class='output co'>#&gt; 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%
+#&gt; </div><div class='input'>
+<span class='va'>limmaTMLEout</span> <span class='op'>&lt;-</span> <span class='fu'>modtest_ic</span><span class='op'>(</span>biotmle <span class='op'>=</span> <span class='va'>biomarkerTMLEout</span><span class='op'>)</span>
+</div></pre>
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