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--- a +++ b/docs/reference/bioTMLE-class.html @@ -0,0 +1,231 @@ +<!-- 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" 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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'>#> <span class='message'>Loading required package: MatrixGenerics</span></div><div class='output co'>#> <span class='message'>Loading required package: matrixStats</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Attaching package: ‘MatrixGenerics’</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:matrixStats’:</span> +#> <span class='message'></span> +#> <span class='message'> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,</span> +#> <span class='message'> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,</span> +#> <span class='message'> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,</span> +#> <span class='message'> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,</span> +#> <span class='message'> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,</span> +#> <span class='message'> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,</span> +#> <span class='message'> colWeightedMeans, colWeightedMedians, colWeightedSds,</span> +#> <span class='message'> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,</span> +#> <span class='message'> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,</span> +#> <span class='message'> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,</span> +#> <span class='message'> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,</span> +#> <span class='message'> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,</span> +#> <span class='message'> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,</span> +#> <span class='message'> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,</span> +#> <span class='message'> rowWeightedSds, rowWeightedVars</span></div><div class='output co'>#> <span class='message'>Loading required package: GenomicRanges</span></div><div class='output co'>#> <span class='message'>Loading required package: stats4</span></div><div class='output co'>#> <span class='message'>Loading required package: BiocGenerics</span></div><div class='output co'>#> <span class='message'>Loading required package: parallel</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Attaching package: ‘BiocGenerics’</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:parallel’:</span> +#> <span class='message'></span> +#> <span class='message'> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,</span> +#> <span class='message'> clusterExport, clusterMap, parApply, parCapply, parLapply,</span> +#> <span class='message'> parLapplyLB, parRapply, parSapply, parSapplyLB</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'> IQR, mad, sd, var, xtabs</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'> anyDuplicated, append, as.data.frame, basename, cbind, colnames,</span> +#> <span class='message'> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,</span> +#> <span class='message'> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,</span> +#> <span class='message'> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,</span> +#> <span class='message'> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,</span> +#> <span class='message'> union, unique, unsplit, which.max, which.min</span></div><div class='output co'>#> <span class='message'>Loading required package: S4Vectors</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Attaching package: ‘S4Vectors’</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'> expand.grid, I, unname</span></div><div class='output co'>#> <span class='message'>Loading required package: IRanges</span></div><div class='output co'>#> <span class='message'>Loading required package: GenomeInfoDb</span></div><div class='output co'>#> <span class='message'>Loading required package: Biobase</span></div><div class='output co'>#> <span class='message'>Welcome to Bioconductor</span> +#> <span class='message'></span> +#> <span class='message'> Vignettes contain introductory material; view with</span> +#> <span class='message'> 'browseVignettes()'. To cite Bioconductor, see</span> +#> <span class='message'> 'citation("Biobase")', and for packages 'citation("pkgname")'.</span></div><div class='output co'>#> <span class='message'></span> +#> <span class='message'>Attaching package: ‘Biobase’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:MatrixGenerics’:</span> +#> <span class='message'></span> +#> <span class='message'> rowMedians</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘package:matrixStats’:</span> +#> <span class='message'></span> +#> <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'><-</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'><-</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'><-</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'><-</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> + +