biotmle / Git / [f1dc6e] /docs/reference/bioTMLE-class.html

Models:
DanielG/
biotmle
Downloads: 3
[f1dc6e]: / docs / reference / bioTMLE-class.html
History
Download this file
232 lines (181 with data), 15.3 kB

<!-- 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>Constructor for class bioTMLE — bioTMLE-class • 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="Constructor for class bioTMLE — bioTMLE-class" />
<meta property="og:description" content="Constructor for class bioTMLE" />




<!-- 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>Constructor for class bioTMLE</h1>
    <small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/utils.R'><code>R/utils.R</code></a></small>
    <div class="hidden name"><code>bioTMLE-class.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Constructor for class bioTMLE</p>
    </div>



    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>class <code>biotmle</code> object, sub-classed from SummarizedExperiment.</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://bioconductor.org/packages/SummarizedExperiment'>SummarizedExperiment</a></span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Loading required package: MatrixGenerics</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: matrixStats</span></div><div class='output co'>#&gt; <span class='message'></span>
#&gt; <span class='message'>Attaching package: ‘MatrixGenerics’</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:matrixStats’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,</span>
#&gt; <span class='message'>    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,</span>
#&gt; <span class='message'>    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,</span>
#&gt; <span class='message'>    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,</span>
#&gt; <span class='message'>    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,</span>
#&gt; <span class='message'>    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,</span>
#&gt; <span class='message'>    colWeightedMeans, colWeightedMedians, colWeightedSds,</span>
#&gt; <span class='message'>    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,</span>
#&gt; <span class='message'>    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,</span>
#&gt; <span class='message'>    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,</span>
#&gt; <span class='message'>    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,</span>
#&gt; <span class='message'>    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,</span>
#&gt; <span class='message'>    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,</span>
#&gt; <span class='message'>    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,</span>
#&gt; <span class='message'>    rowWeightedSds, rowWeightedVars</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: GenomicRanges</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: stats4</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: BiocGenerics</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: parallel</span></div><div class='output co'>#&gt; <span class='message'></span>
#&gt; <span class='message'>Attaching package: ‘BiocGenerics’</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:parallel’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span>
#&gt; <span class='message'>    clusterExport, clusterMap, parApply, parCapply, parLapply,</span>
#&gt; <span class='message'>    parLapplyLB, parRapply, parSapply, parSapplyLB</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:stats’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    IQR, mad, sd, var, xtabs</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:base’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    anyDuplicated, append, as.data.frame, basename, cbind, colnames,</span>
#&gt; <span class='message'>    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,</span>
#&gt; <span class='message'>    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,</span>
#&gt; <span class='message'>    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,</span>
#&gt; <span class='message'>    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,</span>
#&gt; <span class='message'>    union, unique, unsplit, which.max, which.min</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: S4Vectors</span></div><div class='output co'>#&gt; <span class='message'></span>
#&gt; <span class='message'>Attaching package: ‘S4Vectors’</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:base’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    expand.grid, I, unname</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: IRanges</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: GenomeInfoDb</span></div><div class='output co'>#&gt; <span class='message'>Loading required package: Biobase</span></div><div class='output co'>#&gt; <span class='message'>Welcome to Bioconductor</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    Vignettes contain introductory material; view with</span>
#&gt; <span class='message'>    'browseVignettes()'. To cite Bioconductor, see</span>
#&gt; <span class='message'>    'citation("Biobase")', and for packages 'citation("pkgname")'.</span></div><div class='output co'>#&gt; <span class='message'></span>
#&gt; <span class='message'>Attaching package: ‘Biobase’</span></div><div class='output co'>#&gt; <span class='message'>The following object is masked from ‘package:MatrixGenerics’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    rowMedians</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:matrixStats’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'>    anyMissing, rowMedians</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='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='va'>example_biotmle_class</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>se</span><span class='op'>)</span> <span class='op'>{</span>
  <span class='va'>call</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/match.call.html'>match.call</a></span><span class='op'>(</span>expand.dots <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
  <span class='va'>biotmle</span> <span class='op'>&lt;-</span> <span class='fu'>.biotmle</span><span class='op'>(</span>
    <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html'>SummarizedExperiment</a></span><span class='op'>(</span>
      assays <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>assay</a></span><span class='op'>(</span><span class='va'>se</span><span class='op'>)</span>,
      rowData <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html'>rowData</a></span><span class='op'>(</span><span class='va'>se</span><span class='op'>)</span>,
      colData <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'>se</span><span class='op'>)</span>
    <span class='op'>)</span>,
    call <span class='op'>=</span> <span class='va'>call</span>,
    ateOut <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='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='cn'>NA</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span>,
    tmleOut <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span><span class='op'>(</span><span class='cn'>NA</span>, <span class='fl'>10</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span>,
    topTable <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span><span class='op'>(</span><span class='cn'>NA</span>, <span class='fl'>10</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span>
  <span class='op'>)</span>
  <span class='kw'><a href='https://rdrr.io/r/base/function.html'>return</a></span><span class='op'>(</span><span class='va'>biotmle</span><span class='op'>)</span>
<span class='op'>}</span>

<span class='va'>example_class</span> <span class='op'>&lt;-</span> <span class='fu'>example_biotmle_class</span><span class='op'>(</span>se <span class='op'>=</span> <span class='va'>illuminaData</span><span class='op'>)</span>
</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>