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





  
  

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      <a href="../articles/exposureBiomarkers.html">Identifying Biomarkers from an Exposure Variable with `biotmle`</a>





  
  

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    <h1>Constructor for class bioTMLE</h1>





  
  

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    <small class="dont-index">Source: <a href='https://github.com/nhejazi/biotmle/blob/master/R/utils.R'><code>R/utils.R</code></a></small>





  
  

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    <div class="hidden name"><code>bioTMLE-class.Rd</code></div>





  
  

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    <p>Constructor for class bioTMLE</p>





  
  

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





  
  

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    <p>class <code>biotmle</code> object, sub-classed from SummarizedExperiment.</p>





  
  

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    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>





  
  

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    <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>





  
  

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</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>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&gt; <span class='message'>    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,</span>





  
  

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#&gt; <span class='message'>    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,</span>





  
  

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#&gt; <span class='message'>    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,</span>





  
  

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#&gt; <span class='message'>    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,</span>





  
  

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#&gt; <span class='message'>    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,</span>





  
  

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#&gt; <span class='message'>    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,</span>





  
  

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#&gt; <span class='message'>    colWeightedMeans, colWeightedMedians, colWeightedSds,</span>





  
  

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#&gt; <span class='message'>    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,</span>





  
  

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#&gt; <span class='message'>    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,</span>





  
  

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#&gt; <span class='message'>    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,</span>





  
  

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#&gt; <span class='message'>    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,</span>





  
  

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#&gt; <span class='message'>    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,</span>





  
  

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#&gt; <span class='message'>    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,</span>





  
  

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#&gt; <span class='message'>    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,</span>





  
  

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#&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>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&gt; <span class='message'>    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span>





  
  

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#&gt; <span class='message'>    clusterExport, clusterMap, parApply, parCapply, parLapply,</span>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&gt; <span class='message'>    anyDuplicated, append, as.data.frame, basename, cbind, colnames,</span>





  
  

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#&gt; <span class='message'>    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,</span>





  
  

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#&gt; <span class='message'>    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,</span>





  
  

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#&gt; <span class='message'>    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,</span>





  
  

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#&gt; <span class='message'>    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,</span>





  
  

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#&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>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&gt; <span class='message'>    Vignettes contain introductory material; view with</span>





  
  

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#&gt; <span class='message'>    'browseVignettes()'. To cite Bioconductor, see</span>





  
  

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#&gt; <span class='message'>    'citation("Biobase")', and for packages 'citation("pkgname")'.</span></div><div class='output co'>#&gt; <span class='message'></span>





  
  

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#&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>





  
  

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#&gt; <span class='message'></span>





  
  

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#&gt; <span class='message'>    rowMedians</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘package:matrixStats’:</span>





  
  

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#&gt; <span class='message'></span>





  
  

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#&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>





  
  

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<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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<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>





  
  

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  <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>





  
  

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  <span class='va'>biotmle</span> <span class='op'>&lt;-</span> <span class='fu'>.biotmle</span><span class='op'>(</span>





  
  

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    <span class='fu'><a href='https://rdrr.io/pkg/SummarizedExperiment/man/RangedSummarizedExperiment-class.html'>SummarizedExperiment</a></span><span class='op'>(</span>





  
  

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      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>,





  
  

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      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>,





  
  

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      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>





  
  

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    <span class='op'>)</span>,





  
  

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    call <span class='op'>=</span> <span class='va'>call</span>,





  
  

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    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>,





  
  

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    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>,





  
  

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    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>





  
  

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  <span class='op'>)</span>





  
  

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  <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>





  
  

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<span class='op'>}</span>





  
  

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<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>





  
  

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</div></pre>





  
  

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  <p>Developed by Nima Hejazi, Alan Hubbard, Mark van der Laan.</p>





  
  

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