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README.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="viewport" content="width=device-width, initial-scale=1">
<link 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<h1 id="tcga.data-r-package">TCGA.DATA R Package</h1>
<ul>
<li><a href="#package-information">Package information</a>
<ul>
<li><a href="#how-to-use-the-dataset">How to use the dataset</a></li>
</ul></li>
<li><a href="#how-to-build-own-data-package">How to build own data package</a></li>
<li><a href="#ackowledgements">Ackowledgements</a></li>
</ul>
<p>This R Package allows to retrieve Gene Expression, Mutation and clinical data from <a href="http://gdc-portal.nci.nih.gov/">TCGA database</a> (The Cancer Genome Atlas). It retrieves a single type of cancer at a time.</p>
<p>We publish diferent package in the <a href="https://github.com/averissimo/tcga.data/releases">releases page</a> that allow to quickly use the datasets.</p>
<p>The genome expression datasets are already in a matrix format ready to be used. The data is in FPKM (Fragments Per Kilobase Million) format. Any additional normalization to use in models must be performed</p>
<h2 id="package-information">Package information</h2>
<h3 id="how-to-use-the-dataset">How to use the dataset</h3>
<ol>
<li><p>Install <code>brca.data</code> by using <code>devtools</code> package. (<code>brca.data</code>, <code>prad.data</code> or <code>skcm.data</code>)</p></li>
<li><p>Load the library</p></li>
<li>Load the required datasets (one or more of the following)
<ul>
<li><code>multiAssay</code></li>
<li><code>gdc.original</code></li>
</ul></li>
</ol>
<p>In older versions of this package, prior to September 2018, the dataset was named <code>fpkm.per.tissue</code> or <code>mutation</code>, but we since improved the storage using a MultiAssayExperiment object from bioconductor.</p>
<p>To recover the datasets in the old matrix format use the following</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">data</span>(<span class="st">'multiAssay'</span>)
fpkm.data <-<span class="st"> </span><span class="kw">build.matrix</span>(<span class="st">'RNASeqFPKM'</span>, multiAssay)
fpkm.per.tissue <-<span class="st"> </span>fpkm.data<span class="op">$</span>data
fpkm.clinical <-<span class="st"> </span>fpkm.data<span class="op">$</span>clinical</code></pre></div>
<h4 id="example-for-brca-package">Example for BRCA package</h4>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># The library can also be loaded and use the function install_git without 'devtools::' prefix</span>
BiocManager<span class="op">::</span><span class="kw">install</span>(<span class="st">'https://github.com/averissimo/tcga.data/releases/download/2016.12.15-brca/brca.data_1.0.tar.gz'</span>)
<span class="co">#</span>
<span class="co"># Load the brca.data package</span>
<span class="kw">library</span>(brca.data)
<span class="co"># start using the data, for example the tissue data</span>
<span class="kw">data</span>(fpkm.per.tissue)
<span class="co"># tissue is now in the enviromnet and will be loaded on the first</span>
<span class="co"># time it is used. For example:</span>
<span class="kw">names</span>(fpkm.per.tissue)</code></pre></div>
<h2 id="how-to-build-own-data-package">How to build own data package</h2>
<ol>
<li>Open vignettes/build_data.Rmd</li>
<li>Change in the header of the Rmd <em>(beginning of the document)</em> the project param to the target TCGA project</li>
<li>Open DESCRITION and change the name of the package to the desired name</li>
</ol>
<ul>
<li>we use a convention of ####.data where #### is the tcga project name in lowercase</li>
</ul>
<ol>
<li>Run the vignettes/build_data.Rmd to build the cache of the data</li>
<li>Run <code>devtools::document()</code> to create documentation</li>
<li>Run <code>devtools::build()</code> to build the actual package</li>
</ol>
<h2 id="ackowledgements">Ackowledgements</h2>
<p>This package was developed primarily by <em><a href="http://web.tecnico.ulisboa.pt/andre.verissimo/">André Veríssimo</a></em> with support from <em>Marta Lopes</em>, <em>Eunice Carrasquinha</em> and <em><a href="http://web.tecnico.ulisboa.pt/susanavinga/">Susana Vinga</a></em></p>
<p>This work was supported by:</p>
<ul>
<li><a href="www.fct.pt">FCT</a>, through IDMEC, under LAETA, projects <em>(UID/EMS/50022/2013)</em>;</li>
<li>Susana Vinga acknowledges support by program Investigador FCT <em>(IF/00653/2012)</em> from <a href="www.fct.pt">FCT</a>, co-funded by the European Social Fund <em>(ESF)</em> through the Operational Program Human Potential <em>(POPH)</em>;</li>
<li>André Veríssimo acknowledges support from <a href="www.fct.pt">FCT</a> <em>(SFRH/BD/97415/2013)</em>.</li>
</ul>
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