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            <h1 id="seo-header">oncoPredict包进行药物敏感性预测</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="安装包"><a href="#安装包" class="headerlink" title="安装包"></a>安装包</h2><ul>
<li>conda create -n oncoPredict -c conda-forge r-base&#x3D;4.1.3</li>
<li>conda activate oncoPredict</li>
<li>conda install -c conda-forge r-tidyverse -y</li>
<li>conda install -c conda-forge r-irkernel -y</li>
<li>Rscript -e “IRkernel::installspec(name&#x3D;’oncoPredict’, displayname&#x3D;’r-oncoPredict’)”</li>
<li>conda install -c conda-forge r-nloptr -y</li>
<li>conda install -c conda-forge r-lme4 -y</li>
<li>conda install -c conda-forge r-pbkrtest -y</li>
<li>conda install -c conda-forge r-car -y</li>
<li>conda install -c conda-forge r-biocmanager -y</li>
<li>conda install -c conda-forge r-ggpubr -y</li>
<li>conda install -c bioconda bioconductor-maftools -y</li>
<li>BiocManager::install(‘oncoPredict’)</li>
<li>从<a target="_blank" rel="noopener" href="https://osf.io/c6tfx/">oncoPredict作者提供的地址</a>下载整理好的<a target="_blank" rel="noopener" href="http://portals.broadinstitute.org/ctrp.v2.1/">CTRP</a>和<a target="_blank" rel="noopener" href="https://www.cancerrxgene.org/">GDSC</a>，<a target="_blank" rel="noopener" href="https://mp.weixin.qq.com/s?__biz=MzAxMDkxODM1Ng==&mid=2247507359&idx=1&sn=e1b1602338792b6bbd7283bbcc07fe81&scene=21#wechat_redirect">生信技能树的介绍</a>。<a target="_blank" rel="noopener" href="https://share.limour.top/d/data/oncoPredict/DataFiles.zip">镜像</a></li>
<li>unzip DataFiles.zip</li>
</ul>
<h2 id="读入训练数据"><a href="#读入训练数据" class="headerlink" title="读入训练数据"></a>读入训练数据</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>oncoPredict<span class="hljs-punctuation">)</span><br>CTRP2 <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../oncoPredict/DataFiles/DataFiles//Training Data/CTRP2_Expr (TPM, not log transformed).rds&#x27;</span><span class="hljs-punctuation">)</span><br>CTRP2 <span class="hljs-operator">&lt;-</span> log10<span class="hljs-punctuation">(</span>CTRP2<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>GDSC2_Res <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../oncoPredict/DataFiles/DataFiles//Training Data/CTRP2_Res.rds&#x27;</span><span class="hljs-punctuation">)</span><br>GDSC2_Res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">exp</span><span class="hljs-punctuation">(</span>GDSC2_Res<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="读入预测数据"><a href="#读入预测数据" class="headerlink" title="读入预测数据"></a>读入预测数据</h2><p><a href="https://occdn.limour.top/2157.html">f_dedup_IQR</a></p>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs R">load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../DEG/TCGA/PRAD_tp.rda&#x27;</span><span class="hljs-punctuation">)</span><br>tpm <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>assays<span class="hljs-operator">@</span>data<span class="hljs-operator">$</span>tpm_unstrand<br>colnames<span class="hljs-punctuation">(</span>tpm<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>colData<span class="hljs-operator">$</span>patient<br>tpm <span class="hljs-operator">&lt;-</span> tpm<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_rm_duplicated<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>tpm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>geneInfo <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>data<span class="hljs-operator">@</span>rowRanges<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gene_id&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_type&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_name&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>tpm <span class="hljs-operator">&lt;-</span> f_dedup_IQR<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>tpm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> geneInfo<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><br>comm <span class="hljs-operator">&lt;-</span> intersect<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>CTRP2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> rownames<span class="hljs-punctuation">(</span>tpm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>CTRP2 <span class="hljs-operator">&lt;-</span> CTRP2<span class="hljs-punctuation">[</span>comm<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>tpm <span class="hljs-operator">&lt;-</span> tpm<span class="hljs-punctuation">[</span>comm<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>tpm <span class="hljs-operator">&lt;-</span> log10<span class="hljs-punctuation">(</span>tpm<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="进行预测"><a href="#进行预测" class="headerlink" title="进行预测"></a>进行预测</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>oncoPredict<span class="hljs-punctuation">)</span><br>load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;oncoPredict_calcPhenotype.rdata&#x27;</span><span class="hljs-punctuation">)</span><br>keep <span class="hljs-operator">&lt;-</span> rowSums<span class="hljs-punctuation">(</span>CTRP2<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">0.8</span><span class="hljs-operator">*</span>ncol<span class="hljs-punctuation">(</span>CTRP2<span class="hljs-punctuation">)</span><br>calcPhenotype<span class="hljs-punctuation">(</span>trainingExprData <span class="hljs-operator">=</span> CTRP2<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>              trainingPtype <span class="hljs-operator">=</span> GDSC2_Res<span class="hljs-punctuation">,</span><br>              testExprData <span class="hljs-operator">=</span> as.matrix<span class="hljs-punctuation">(</span>tpm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>              batchCorrect <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;eb&#x27;</span><span class="hljs-punctuation">,</span>  <span class="hljs-comment">#   &quot;eb&quot; for ComBat  </span><br>              powerTransformPhenotype <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span><br>              removeLowVaryingGenes <span class="hljs-operator">=</span> <span class="hljs-number">0.2</span><span class="hljs-punctuation">,</span><br>              minNumSamples <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> <br>              printOutput <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> <br>              removeLowVaringGenesFrom <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;rawData&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<ul>
<li>save(CTRP2, GDSC2_Res, tpm, file &#x3D; ‘oncoPredict_calcPhenotype.rdata’)</li>
<li>nano oncoPredict_calcPhenotype.R</li>
<li>conda activate oncoPredict</li>
<li>Rscript .&#x2F;oncoPredict_calcPhenotype.R –max-ppsize&#x3D;500000</li>
</ul>
<h2 id="预测结果可视化"><a href="#预测结果可视化" class="headerlink" title="预测结果可视化"></a>预测结果可视化</h2><h3 id="读入预测结果"><a href="#读入预测结果" class="headerlink" title="读入预测结果"></a>读入预测结果</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">testPtype <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;./calcPhenotype_Output/DrugPredictions.csv&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>testPtype <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>testPtype<span class="hljs-punctuation">)</span><br>testPtype<br></code></pre></td></tr></table></figure>

<h3 id="贴上分组"><a href="#贴上分组" class="headerlink" title="贴上分组"></a>贴上分组</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs R">group <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../fig5/tcga.predict.rds&#x27;</span><span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>testPtype<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;CIL55&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;BRD4132&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>group<span class="hljs-operator">$</span>group<span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[[</span>ncol<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;Risk Group&#x27;</span><br>df<br></code></pre></td></tr></table></figure>

<h3 id="绘图"><a href="#绘图" class="headerlink" title="绘图"></a>绘图</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>ggpubr<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">4</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><br>my_comparisons <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Low Risk&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;High Risk&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>ggviolin<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> x<span class="hljs-operator">=</span><span class="hljs-string">&quot;Risk Group&quot;</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-string">&quot;CIL55&quot;</span><span class="hljs-punctuation">,</span> fill <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Risk Group&quot;</span><span class="hljs-punctuation">,</span> <br>palette <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#00AFBB&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;#E7B800&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br>add <span class="hljs-operator">=</span> <span class="hljs-string">&quot;boxplot&quot;</span><span class="hljs-punctuation">,</span> add.params <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>fill<span class="hljs-operator">=</span><span class="hljs-string">&quot;white&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span> <br>stat_compare_means<span class="hljs-punctuation">(</span>comparisons <span class="hljs-operator">=</span> my_comparisons<span class="hljs-punctuation">,</span> label <span class="hljs-operator">=</span> <span class="hljs-string">&quot;p.signif&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-comment">#label这里表示选择显著性标记（星号） </span><br></code></pre></td></tr></table></figure>
                
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