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            <h1 id="seo-header">TCGAbiolinks (三）获取全面的临床数据 </h1>
            
            
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                <h2 id="基础数据获取"><a href="#基础数据获取" class="headerlink" title="基础数据获取"></a>基础数据获取</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>TCGAbiolinks<span class="hljs-punctuation">)</span><br>PRAD <span class="hljs-operator">&lt;-</span> GDCquery<span class="hljs-punctuation">(</span>project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;TCGA-PRAD&#x27;</span><span class="hljs-punctuation">,</span><br>                  data.category <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Clinical&quot;</span><span class="hljs-punctuation">,</span><br>                  file.type <span class="hljs-operator">=</span> <span class="hljs-string">&quot;xml&quot;</span><span class="hljs-punctuation">)</span><br>GDCdownload<span class="hljs-punctuation">(</span>query <span class="hljs-operator">=</span> PRAD<span class="hljs-punctuation">)</span><br><span class="hljs-operator">?</span> GDCprepare_clinic<br>clinical.info <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;admin&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;patient&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;stage_event&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;new_tumor_event&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 不获取&#x27;drug&#x27;, &#x27;follow_up&#x27;, &#x27;radiation&#x27;</span><br>clinical.info<br>f_rm_colN <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> regex<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    df<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-operator">!</span>grepl<span class="hljs-punctuation">(</span>regex<span class="hljs-punctuation">,</span> colnames<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br>f_rm_duplicated <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">,</span> reverse<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>reverse<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    which<span class="hljs-punctuation">(</span>NameL <span class="hljs-operator">%in%</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>clinical <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>info <span class="hljs-keyword">in</span> clinical.info<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    clinical<span class="hljs-punctuation">[[</span>info<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> GDCprepare_clinic<span class="hljs-punctuation">(</span>PRAD<span class="hljs-punctuation">,</span> clinical.info <span class="hljs-operator">=</span> info<span class="hljs-punctuation">)</span><br>    clinical<span class="hljs-punctuation">[[</span>info<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> f_rm_colN<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">[[</span>info<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;project&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>clinical<span class="hljs-operator">$</span>admin <span class="hljs-operator">&lt;-</span> f_rm_colN<span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>admin<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;file_uuid&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>info <span class="hljs-keyword">in</span> clinical.info<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    clinical<span class="hljs-punctuation">[[</span>info<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">[[</span>info<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_merge  <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_mergedList<span class="hljs-punctuation">,</span> by<span class="hljs-punctuation">,</span> <span class="hljs-built_in">all</span><span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    Reduce<span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span> merge<span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">,</span> by<span class="hljs-operator">=</span>by<span class="hljs-punctuation">,</span> <span class="hljs-built_in">all</span><span class="hljs-operator">=</span><span class="hljs-built_in">all</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> lc_mergedList<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>clinical <span class="hljs-operator">&lt;-</span> f_merge<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> by <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;bcr_patient_barcode&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">all</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>clinical<br></code></pre></td></tr></table></figure>

<h2 id="数据更新补丁"><a href="#数据更新补丁" class="headerlink" title="数据更新补丁"></a>数据更新补丁</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></pre></td><td class="code"><pre><code class="hljs R">cl_new <span class="hljs-operator">&lt;-</span> GDCquery_clinic<span class="hljs-punctuation">(</span>project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;TCGA-PRAD&#x27;</span><span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;clinical&#x27;</span><span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> merge<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> cl_new<span class="hljs-punctuation">,</span> by <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;bcr_patient_barcode&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">all</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> suffixes <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;.old&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;.new&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>clinical<br></code></pre></td></tr></table></figure>

<h2 id="生存分析补丁"><a href="#生存分析补丁" class="headerlink" title="生存分析补丁"></a>生存分析补丁</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></pre></td><td class="code"><pre><code class="hljs R">clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;os_status&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span>vital_status.new <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;Dead&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 0表示因病死亡</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;os_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span>os_status <span class="hljs-operator">==</span> <span class="hljs-number">0</span><span class="hljs-punctuation">,</span> days_to_death.new<span class="hljs-punctuation">,</span> days_to_last_follow_up<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">$</span>os_time<span class="hljs-punctuation">)</span><br>clinical<span class="hljs-punctuation">[</span>clinical<span class="hljs-operator">$</span>patient_death_reason <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;Other, non-malignant disease&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;os_status&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>os_status<span class="hljs-punctuation">)</span><br> <br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;dcf_status&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span>new_neoplasm_event_type <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 1表示有新的肿瘤事件</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;dcf_status&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>dcf_status<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">,</span> dcf_status<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 1表示有新的肿瘤事件</span><br>clinical<span class="hljs-punctuation">[</span>clinical<span class="hljs-operator">$</span>biochemical_recurrence <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;YES&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;dcf_status&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>dcf_status<span class="hljs-punctuation">)</span><br> <br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;tmp_dcf_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;days_to_first_biochemical_recurrence&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;tmp_dcf_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>tmp_dcf_time<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> os_time<span class="hljs-punctuation">,</span> tmp_dcf_time<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>tmp_dcf_time<span class="hljs-punctuation">)</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;dcf_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span>dcf_status <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> days_to_new_tumor_event_after_initial_treatment<span class="hljs-punctuation">,</span> tmp_dcf_time<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;dcf_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>dcf_time<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> tmp_dcf_time<span class="hljs-punctuation">,</span> dcf_time<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">$</span>dcf_time<span class="hljs-punctuation">)</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;dcf_time&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> with<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> ifelse<span class="hljs-punctuation">(</span>biochemical_recurrence <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;YES&#x27;</span><span class="hljs-punctuation">,</span> tmp_dcf_time<span class="hljs-punctuation">,</span> dcf_time<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>dcf_time<span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> f_rm_colN<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;tmp_dcf_time&quot;</span><span class="hljs-punctuation">)</span><br>write.csv<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;TCGA-PRAD_clinical.csv&#x27;</span><span class="hljs-punctuation">)</span><br> <br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>os_status<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>os_time<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>dcf_status<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>dcf_time<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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