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| 43 | <meta property="og:description" content="Histogram of raw or FDR-adjusted p-values from the moderated t-test." /> |
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| 123 | <h1>Plot p-values from moderated statistical tests for class biotmle</h1> |
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| 124 | <small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/plots.R'><code>R/plots.R</code></a></small> |
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| 125 | <div class="hidden name"><code>plot.bioTMLE.Rd</code></div> |
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| 126 | </div> |
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| 127 | |||
| 128 | <div class="ref-description"> |
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| 129 | <p>Histogram of raw or FDR-adjusted p-values from the moderated t-test.</p> |
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| 130 | </div> |
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| 131 | |||
| 132 | <pre class="usage"><span class='co'># S3 method for bioTMLE</span> |
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| 133 | <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span>, type <span class='op'>=</span> <span class='st'>"pvals_adj"</span><span class='op'>)</span></pre> |
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| 134 | |||
| 135 | <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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| 136 | <table class="ref-arguments"> |
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| 137 | <colgroup><col class="name" /><col class="desc" /></colgroup> |
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| 138 | <tr> |
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| 139 | <th>x</th> |
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| 140 | <td><p>object of class <code>biotmle</code> as produced by an appropriate call |
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| 141 | to <code>biomarkertmle</code></p></td> |
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| 142 | </tr> |
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| 143 | <tr> |
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| 144 | <th>...</th> |
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| 145 | <td><p>additional arguments passed <code>plot</code> as necessary</p></td> |
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| 146 | </tr> |
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| 147 | <tr> |
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| 148 | <th>type</th> |
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| 149 | <td><p>character describing whether to provide a plot of unadjusted or |
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| 150 | adjusted p-values (adjustment performed via Benjamini-Hochberg)</p></td> |
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| 151 | </tr> |
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| 152 | </table> |
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| 153 | |||
| 154 | <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
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| 155 | |||
| 156 | <p>object of class <code>ggplot</code> containing a histogram of the raw or |
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| 157 | Benjamini-Hochberg corrected p-values (depending on user input).</p> |
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| 158 | |||
| 159 | <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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| 160 | <pre class="examples"><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>{</span> |
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| 161 | <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> |
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| 162 | <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> |
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| 163 | <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> |
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| 164 | <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> |
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| 165 | <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> |
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| 166 | |||
| 167 | <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='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> |
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| 168 | <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'>%>%</span> |
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| 169 | <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'>></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'>%>%</span> |
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| 170 | <span class='fu'>DataFrame</span><span class='op'>(</span><span class='op'>)</span> |
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| 171 | <span class='va'>benz_idx</span> <span class='op'><-</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> |
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| 172 | |||
| 173 | <span class='va'>biomarkerTMLEout</span> <span class='op'><-</span> <span class='fu'><a href='biomarkertmle.html'>biomarkertmle</a></span><span class='op'>(</span> |
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| 174 | se <span class='op'>=</span> <span class='va'>illuminaData</span>, |
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| 175 | varInt <span class='op'>=</span> <span class='va'>benz_idx</span>, |
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| 176 | 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>, |
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| 177 | 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>, |
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| 178 | 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> |
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| 179 | <span class='op'>)</span> |
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| 180 | |||
| 181 | <span class='va'>limmaTMLEout</span> <span class='op'><-</span> <span class='fu'><a href='modtest_ic.html'>modtest_ic</a></span><span class='op'>(</span>biotmle <span class='op'>=</span> <span class='va'>biomarkerTMLEout</span><span class='op'>)</span> |
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| 182 | |||
| 183 | <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>limmaTMLEout</span>, type <span class='op'>=</span> <span class='st'>"pvals_adj"</span><span class='op'>)</span> |
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| 184 | <span class='op'>}</span> |
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| 185 | </div></pre> |
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| 186 | </div> |
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| 197 | <p>Developed by Nima Hejazi, Alan Hubbard, Mark van der Laan.</p> |
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