<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Biomarker Evaluation with Targeted Minimum Loss Estimation of the ATE — biomarkertmle • biotmle</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/readable/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Biomarker Evaluation with Targeted Minimum Loss Estimation of the ATE — biomarkertmle" />
<meta property="og:description" content="Computes the causal target parameter defined as the difference between the
biomarker expression values under treatment and those same values under no
treatment, using Targeted Minimum Loss Estimation." />
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">biotmle</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.17.0</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/exposureBiomarkers.html">Identifying Biomarkers from an Exposure Variable with `biotmle`</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/nhejazi/biotmle/">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Biomarker Evaluation with Targeted Minimum Loss Estimation of the ATE</h1>
<small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/biotmle.R'><code>R/biotmle.R</code></a></small>
<div class="hidden name"><code>biomarkertmle.Rd</code></div>
</div>
<div class="ref-description">
<p>Computes the causal target parameter defined as the difference between the
biomarker expression values under treatment and those same values under no
treatment, using Targeted Minimum Loss Estimation.</p>
</div>
<pre class="usage"><span class='fu'>biomarkertmle</span><span class='op'>(</span>
<span class='va'>se</span>,
<span class='va'>varInt</span>,
normalized <span class='op'>=</span> <span class='cn'>TRUE</span>,
ngscounts <span class='op'>=</span> <span class='cn'>FALSE</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/MulticoreParam-class.html'>MulticoreParam</a></span><span class='op'>(</span><span class='op'>)</span>,
bppar_debug <span class='op'>=</span> <span class='cn'>FALSE</span>,
cv_folds <span class='op'>=</span> <span class='fl'>1</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='st'>"SL.bayesglm"</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.bayesglm"</span>, <span class='st'>"SL.earth"</span>, <span class='st'>"SL.ranger"</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>se</th>
<td><p>A <code>SummarizedExperiment</code> containing microarray expression
or next-generation sequencing data in the <code>assays</code> slot and a matrix
of phenotype-level data in the <code>colData</code> slot.</p></td>
</tr>
<tr>
<th>varInt</th>
<td><p>A <code>numeric</code> indicating the column of the design matrix
corresponding to the treatment or outcome of interest (in the
<code>colData</code> slot of the <code>SummarizedExperiment</code> argument "se").</p></td>
</tr>
<tr>
<th>normalized</th>
<td><p>A <code>logical</code> indicating whether the data included in
the <code>assay</code> slot of the input <code>SummarizedExperiment</code> object has
been normalized externally. The default is set to <code>TRUE</code> with the
expectation that an appropriate normalization method has been applied. If
set to <code>FALSE</code>, median normalization is performed for microarray data.</p></td>
</tr>
<tr>
<th>ngscounts</th>
<td><p>A <code>logical</code> indicating whether the data are counts
generated from a next-generation sequencing experiment (e.g., RNA-seq). The
default setting assumes continuous expression measures as generated by
microarray platforms.</p></td>
</tr>
<tr>
<th>bppar_type</th>
<td><p>A parallelization option specified by <code>BiocParallel</code>.
Consult the manual page for <code><a href='https://rdrr.io/pkg/BiocParallel/man/BiocParallelParam-class.html'>BiocParallelParam</a></code>
for possible types and their descriptions. The default for this argument is
<code><a href='https://rdrr.io/pkg/BiocParallel/man/MulticoreParam-class.html'>MulticoreParam</a></code>, for multicore evaluation.</p></td>
</tr>
<tr>
<th>bppar_debug</th>
<td><p>A <code>logical</code> indicating whether or not to rely upon
pkgBiocParallel. Setting this argument to <code>TRUE</code>, replaces the call
to <code><a href='https://rdrr.io/pkg/BiocParallel/man/bplapply.html'>bplapply</a></code> by a call to <code>lapply</code>, which
significantly reduces the overhead of debugging. Note that invoking this
option overrides all other parallelization arguments.</p></td>
</tr>
<tr>
<th>cv_folds</th>
<td><p>A <code>numeric</code> scalar indicating how many folds to use in
performing targeted minimum loss estimation. Cross-validated estimates have
been demonstrated to allow relaxation of certain theoretical conditions and
and accommodate the construction of more conservative variance estimates.</p></td>
</tr>
<tr>
<th>g_lib</th>
<td><p>A <code>character</code> vector specifying the library of machine
learning algorithms for use in fitting the propensity score P(A = a | W).</p></td>
</tr>
<tr>
<th>Q_lib</th>
<td><p>A <code>character</code> vector specifying the library of machine
learning algorithms for use in fitting the outcome regression E[Y | A,W].</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Additional arguments to be passed to <code><a href='https://rdrr.io/pkg/drtmle/man/drtmle.html'>drtmle</a></code>
in computing the targeted minimum loss estimator of the average treatment
effect.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>S4 object of class <code>biotmle</code>, inheriting from
<code>SummarizedExperiment</code>, with additional slots <code>tmleOut</code> and
<code>call</code>, among others, containing TML estimates of the ATE of exposure
on biomarker expression.</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>
</div><div class='output co'>#> <span class='message'></span>
#> <span class='message'>Attaching package: ‘dplyr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:Biobase’:</span>
#> <span class='message'></span>
#> <span class='message'> combine</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:GenomicRanges’:</span>
#> <span class='message'></span>
#> <span class='message'> intersect, setdiff, union</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:GenomeInfoDb’:</span>
#> <span class='message'></span>
#> <span class='message'> intersect</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:IRanges’:</span>
#> <span class='message'></span>
#> <span class='message'> collapse, desc, intersect, setdiff, slice, union</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:S4Vectors’:</span>
#> <span class='message'></span>
#> <span class='message'> first, intersect, rename, setdiff, setequal, union</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:BiocGenerics’:</span>
#> <span class='message'></span>
#> <span class='message'> combine, intersect, setdiff, union</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:matrixStats’:</span>
#> <span class='message'></span>
#> <span class='message'> count</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:stats’:</span>
#> <span class='message'></span>
#> <span class='message'> filter, lag</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:base’:</span>
#> <span class='message'></span>
#> <span class='message'> intersect, setdiff, setequal, union</span></div><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'>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>
</div><div class='output co'>#> <span class='message'>Loading required package: nnls</span></div><div class='output co'>#> <span class='message'>Loading required package: gam</span></div><div class='output co'>#> <span class='message'>Loading required package: splines</span></div><div class='output co'>#> <span class='message'>Loading required package: foreach</span></div><div class='output co'>#> <span class='message'>Loaded gam 1.20</span></div><div class='output co'>#> <span class='message'>Super Learner</span></div><div class='output co'>#> <span class='message'>Version: 2.0-28</span></div><div class='output co'>#> <span class='message'>Package created on 2021-05-04</span></div><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://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'><-</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='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>
<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>
<span class='fu'>DataFrame</span><span class='op'>(</span><span class='op'>)</span>
<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>
<span class='va'>biomarkerTMLEout</span> <span class='op'><-</span> <span class='fu'>biomarkertmle</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'>#>
|
| | 0%</div><div class='output co'>#> <span class='message'>Loading required package: quadprog</span></div><div class='output co'>#> <span class='message'>Loading required package: nloptr</span></div><div class='output co'>#>
|
|=================================== | 50%
|
|======================================================================| 100%
#> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Nima Hejazi, Alan Hubbard, Mark van der Laan.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
Datasets
Models
