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            <h1 id="seo-header">将多数据集转化成无依赖的数据格式，进行单变量COXPH，并进行RRA整合</h1>
            
            
              <div class="markdown-body">
                
                <h2 id="PCaDB"><a href="#PCaDB" class="headerlink" title="PCaDB"></a>PCaDB</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><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br></pre></td><td class="code"><pre><code class="hljs R">ano <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../DEG/PCaDB/PCaDB_Gene_Annotation.RDS&#x27;</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../DEG/PCaDB/CPC-Gene_eSet.RDS&#x27;</span><span class="hljs-punctuation">)</span><br>tmp<br>clinical <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">@</span>phenoData<span class="hljs-operator">@</span>data<br>clinical <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>bcr_status<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>bcr_status<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>time_to_bcr<span class="hljs-punctuation">)</span><br>expr <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>exprs<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>expr <span class="hljs-operator">&lt;-</span> f_dedup_IQR<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ano<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><br>expr <span class="hljs-operator">&lt;-</span> scale<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>expr <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>colSums<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>expr<br>clinical <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span> <span class="hljs-operator">%in%</span> rownames<span class="hljs-punctuation">(</span>expr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>bcr_status<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>time_to_bcr<span class="hljs-punctuation">)</span><br>clinical<br>expr <span class="hljs-operator">&lt;-</span> expr<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>expr<br>clinical<span class="hljs-operator">$</span>pfs_status <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-operator">$</span>bcr_status<br>clinical<span class="hljs-operator">$</span>pfs_time <span class="hljs-operator">&lt;-</span>  clinical<span class="hljs-operator">$</span>time_to_bcr<br>data <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>data<span class="hljs-operator">$</span>data <span class="hljs-operator">&lt;-</span> expr<br>data<span class="hljs-operator">$</span>meta  <span class="hljs-operator">&lt;-</span> clinical<br>saveRDS<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;CPC-Gene.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="TCGA"><a href="#TCGA" class="headerlink" title="TCGA"></a>TCGA</h2><p><a href="https://occdn.limour.top/2159.html">f_counts2TMM</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><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br></pre></td><td class="code"><pre><code class="hljs R">tmp <span class="hljs-operator">&lt;-</span> load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../DEG/TCGA/PRAD_tp.rda&#x27;</span><span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>assays<span class="hljs-operator">@</span>data<span class="hljs-operator">$</span>unstranded<br>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>colData<span class="hljs-operator">$</span>patient<br>counts <span class="hljs-operator">&lt;-</span> counts<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_rm_duplicated<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>counts<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>counts <span class="hljs-operator">&lt;-</span> f_dedup_IQR<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> geneInfo<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><br>counts<br>counts <span class="hljs-operator">&lt;-</span> f_counts2TMM<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> log2<span class="hljs-punctuation">(</span>counts <span class="hljs-operator">+</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> scale<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>colSums<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>counts<br>clinical <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../DEG/TCGA/clinical/TCGA_PRAD_with_ICGC.rds&#x27;</span><span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span> <span class="hljs-operator">%in%</span> rownames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>new_dcf_status<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>new_dcf_time<span class="hljs-punctuation">)</span><br>clinical<br>counts <span class="hljs-operator">&lt;-</span> counts<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>counts<br>clinical<span class="hljs-operator">$</span>pfs_status <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-operator">$</span>new_dcf_status<br>clinical<span class="hljs-operator">$</span>pfs_time <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>new_dcf_time <span class="hljs-operator">/</span> <span class="hljs-number">365</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><br>data <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>data<span class="hljs-operator">$</span>data <span class="hljs-operator">&lt;-</span> expr<br>data<span class="hljs-operator">$</span>meta  <span class="hljs-operator">&lt;-</span> clinical<br>saveRDS<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;PRAD.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="train-sets"><a href="#train-sets" class="headerlink" title="train_sets"></a>train_sets</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></pre></td><td class="code"><pre><code class="hljs R">train_sets <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>train_sets<span class="hljs-operator">$</span>CPGEA <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;data/CPGEA.rds&#x27;</span><span class="hljs-punctuation">)</span><br>train_sets<span class="hljs-operator">$</span>PRAD <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;data/PRAD.rds&#x27;</span><span class="hljs-punctuation">)</span><br>train_sets<span class="hljs-operator">$</span>mCPRC <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;data/mCRPC.rds&#x27;</span><span class="hljs-punctuation">)</span><br>train_sets<span class="hljs-operator">$</span>DKFZ <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;data/DKFZ.rds&#x27;</span><span class="hljs-punctuation">)</span><br>train_sets<span class="hljs-operator">$</span>GSE54460 <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;data/GSE54460.rds&#x27;</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>train_sets<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;train_sets.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="单变量COXPH"><a href="#单变量COXPH" class="headerlink" title="单变量COXPH"></a>单变量COXPH</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><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;survival&quot;</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;survminer&quot;</span><span class="hljs-punctuation">)</span><br>f_DEG_coxph_oneGene <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>trainSet<span class="hljs-punctuation">,</span> geneN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span><span class="hljs-punctuation">(</span>geneN <span class="hljs-operator">%in%</span> colnames<span class="hljs-punctuation">(</span>trainSet<span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> geneN<span class="hljs-punctuation">,</span> mean<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> lower<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> upper<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> Pvalue<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> VarName<span class="hljs-operator">=</span>geneN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>trainSet<span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span>geneN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>trainSet<span class="hljs-operator">$</span>meta<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pfs_status&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;pfs_time&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    coxmf <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Surv(pfs_time, pfs_status==1)~&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;`&#x27;</span><span class="hljs-punctuation">,</span>geneN<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;`&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     print(coxmf)</span><br>    res.cox <span class="hljs-operator">&lt;-</span> coxph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span>  df<span class="hljs-punctuation">)</span><br>    tmp_res <span class="hljs-operator">&lt;-</span> summary<span class="hljs-punctuation">(</span>res.cox<span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>tmp_res<span class="hljs-operator">$</span>conf.int<span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> res<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-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    colnames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;mean&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;lower&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;upper&#x27;</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Pvalue&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp_res<span class="hljs-operator">$</span>coefficients<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pr(&gt;z)&#x27;</span><span class="hljs-punctuation">]</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;VarName&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_DEG_coxph <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>trainSet<span class="hljs-punctuation">,</span> geneList<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>gene <span class="hljs-keyword">in</span> geneList<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span>f_DEG_coxph_oneGene<span class="hljs-punctuation">(</span>trainSet<span class="hljs-punctuation">,</span> gene<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_DEG_coxph_Sets <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>trainSets<span class="hljs-punctuation">,</span> geneList<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>trainSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-punctuation">[[</span>Name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> f_DEG_coxph<span class="hljs-punctuation">(</span>trainSets<span class="hljs-punctuation">[[</span>Name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> geneList<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br> <br>DEG <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../DEG/TCGA/mCRPC_DEG.rds&#x27;</span><span class="hljs-punctuation">)</span><br>DEG <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>DEG<span class="hljs-punctuation">,</span> padj <span class="hljs-operator">&lt;</span> <span class="hljs-number">0.05</span> <span class="hljs-operator">&amp;</span> <span class="hljs-built_in">abs</span><span class="hljs-punctuation">(</span>log2FoldChange<span class="hljs-punctuation">)</span><span class="hljs-operator">&gt;</span><span class="hljs-number">2</span> <span class="hljs-operator">&amp;</span> <span class="hljs-operator">!</span>grepl<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pseudogene&#x27;</span><span class="hljs-punctuation">,</span> gene_type<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>train_sets <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;train_sets.rds&#x27;</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> f_DEG_coxph_Sets<span class="hljs-punctuation">(</span>train_sets<span class="hljs-punctuation">,</span> unique<span class="hljs-punctuation">(</span>DEG<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;mCRPC.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="RRA聚合"><a href="#RRA聚合" class="headerlink" title="RRA聚合"></a>RRA聚合</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><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br></pre></td><td class="code"><pre><code class="hljs R">tmp <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;mCRPC.rds&#x27;</span><span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>RobustRankAggreg<span class="hljs-punctuation">)</span><br>f_dflist_RRA <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">,</span> N<span class="hljs-punctuation">,</span> orderN<span class="hljs-punctuation">,</span> decreasing<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> dflist<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>        <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[[</span>orderN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>decreasing <span class="hljs-operator">=</span> decreasing<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    aggregateRanks<span class="hljs-punctuation">(</span>glist <span class="hljs-operator">=</span> res<span class="hljs-punctuation">,</span> N <span class="hljs-operator">=</span> N<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>tmp<span class="hljs-operator">$</span>CPGEA<br>r <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> Pvalue<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&amp;</span> mean <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;VarName&#x27;</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>CPGEA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;mean&#x27;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> Score<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><br>r_up <span class="hljs-operator">&lt;-</span> r<br>r <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> Pvalue<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&amp;</span> mean <span class="hljs-operator">&lt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;VarName&#x27;</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>CPGEA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;mean&#x27;</span><span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> Score<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><br>r_down <span class="hljs-operator">&lt;-</span> r<br> <br>r_up<span class="hljs-operator">$</span>Score <span class="hljs-operator">&lt;-</span> log1p<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">/</span>r_up<span class="hljs-operator">$</span>Score<span class="hljs-punctuation">)</span><br>r_down<span class="hljs-operator">$</span>Score <span class="hljs-operator">&lt;-</span> log1p<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">/</span>r_down<span class="hljs-operator">$</span>Score<span class="hljs-punctuation">)</span><br>r_down<span class="hljs-operator">$</span>Score <span class="hljs-operator">&lt;-</span> <span class="hljs-operator">-</span>r_down<span class="hljs-operator">$</span>Score<br>r <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>r_up<span class="hljs-punctuation">,</span>r_down<span class="hljs-punctuation">)</span><br>r <span class="hljs-operator">&lt;-</span> r<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>r<span class="hljs-operator">$</span>Score<span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>r<br>saveRDS<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;mCRPC_RRA.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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