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            <h1 id="seo-header">COX-Ridge：外部数据集验证</h1>
            
            
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                <h2 id="建模"><a href="#建模" class="headerlink" title="建模"></a>建模</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>glmnet<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>df1 <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../fig.3/B_ref_A_fiig.3_C/new_df1.rds&#x27;</span><span class="hljs-punctuation">)</span><br>y <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">[</span><span class="hljs-number">9</span><span class="hljs-operator">:</span><span class="hljs-number">10</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>x <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">8</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>Ridge <span class="hljs-operator">&lt;-</span> glmnet<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> x<span class="hljs-punctuation">,</span> y <span class="hljs-operator">=</span> y<span class="hljs-punctuation">,</span> family <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;cox&#x27;</span><span class="hljs-punctuation">,</span> alpha <span class="hljs-operator">=</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>Ridge<span class="hljs-punctuation">,</span> xvar <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;lambda&#x27;</span><span class="hljs-punctuation">,</span> label <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>Ridge.cv <span class="hljs-operator">&lt;-</span> cv.glmnet<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span>y<span class="hljs-punctuation">,</span>family<span class="hljs-operator">=</span><span class="hljs-string">&quot;cox&quot;</span><span class="hljs-punctuation">,</span> alpha<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span>nfolds<span class="hljs-operator">=</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span> type.measure <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;C&#x27;</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>Ridge.cv<span class="hljs-punctuation">)</span><br>Ridge.cf <span class="hljs-operator">&lt;-</span> coef<span class="hljs-punctuation">(</span>Ridge.cv<span class="hljs-punctuation">,</span> s<span class="hljs-operator">=</span><span class="hljs-string">&quot;lambda.min&quot;</span><span class="hljs-punctuation">)</span><br>Ridge.cf <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>as.matrix<span class="hljs-punctuation">(</span>Ridge.cf<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>Ridge.cf<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;coef&#x27;</span><br>saveRDS<span class="hljs-punctuation">(</span>Ridge.cf<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Ridge.cf.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="验证"><a href="#验证" class="headerlink" title="验证"></a>验证</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><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</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>library<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;rms&quot;</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;../../../COXPH/train_sets.rds&#x27;</span><span class="hljs-punctuation">)</span><br>test_sets <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../COXPH/test/test_sets.rds&#x27;</span><span class="hljs-punctuation">)</span><br>all_sets <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>train_sets<span class="hljs-punctuation">,</span> test_sets<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survminer<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggpubr<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>survRM2<span class="hljs-punctuation">)</span><br>f_surv <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> isplot<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> timeN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;time&#x27;</span><span class="hljs-punctuation">,</span> statusN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;status&#x27;</span><span class="hljs-punctuation">,</span> groupN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;group&#x27;</span><span class="hljs-punctuation">,</span> tau<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span> risk.table<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> ncensor.plot<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>    my.surv <span class="hljs-operator">&lt;&lt;-</span> Surv<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>timeN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">[[</span>statusN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">==</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    my.surv.f <span class="hljs-operator">&lt;&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;my.surv~&quot;</span><span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><br>    my.surv.df <span class="hljs-operator">&lt;&lt;-</span> df<br>    kmfit <span class="hljs-operator">&lt;-</span> surv_fit<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>my.surv.f<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> my.surv.df<span class="hljs-punctuation">)</span><br>    sdiff <span class="hljs-operator">&lt;-</span> survdiff<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>my.surv.f<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> my.surv.df<span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>pv <span class="hljs-operator">&lt;-</span> 1 <span class="hljs-operator">-</span> pchisq<span class="hljs-punctuation">(</span>sdiff<span class="hljs-operator">$</span>chisq<span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>sdiff<span class="hljs-operator">$</span>n<span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>isplot<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-operator">$</span>plot <span class="hljs-operator">&lt;-</span> ggsurvplot<span class="hljs-punctuation">(</span>kmfit<span class="hljs-punctuation">,</span> conf.int <span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> pval <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> risk.table <span class="hljs-operator">=</span> risk.table<span class="hljs-punctuation">,</span> ncensor.plot <span class="hljs-operator">=</span> ncensor.plot<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<span class="hljs-operator">$</span>RMS <span class="hljs-operator">&lt;-</span> rmst2<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>timeN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">[[</span>statusN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> tau<span class="hljs-operator">=</span>tau<span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>RMST <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>rbind<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>RMS<span class="hljs-operator">$</span>RMST.arm1<span class="hljs-operator">$</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>res<span class="hljs-operator">$</span>RMS<span class="hljs-operator">$</span>RMST.arm0<span class="hljs-operator">$</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    rownames<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>RMST<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;RMST (arm=1)&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;RMST (arm=0)&#x27;</span><span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_COXPH_predict <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>data_sets<span class="hljs-punctuation">,</span> coxM<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>data_sets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        try<span class="hljs-punctuation">(</span>expr <span class="hljs-operator">=</span> <span class="hljs-punctuation">&#123;</span><br>            dat <span class="hljs-operator">&lt;-</span> data_sets<span class="hljs-punctuation">[[</span>Name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>            y <span class="hljs-operator">&lt;-</span> Surv<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_time<span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_status <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>            y <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><br>            x <span class="hljs-operator">&lt;-</span> predict<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;lp&quot;</span><span class="hljs-punctuation">,</span>newdata<span class="hljs-operator">=</span>dat<span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><br>            df <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>cbind<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span>y<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>            <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;Risk_Score&#x27;</span><br>            df<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;Low Risk&#x27;</span><br>            df<span class="hljs-operator">$</span>group<span class="hljs-punctuation">[</span>df<span class="hljs-operator">$</span>Risk_Score <span class="hljs-operator">&gt;</span> median<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>Risk_Score<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;High Risk&#x27;</span><br>            df<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> as.factor<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>group<span class="hljs-punctuation">)</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> df<br>        <span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span> <br>f_surv_list  <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df_lists<span class="hljs-punctuation">,</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>df_lists<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        df <span class="hljs-operator">&lt;-</span> df_lists<span class="hljs-punctuation">[[</span>Name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</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_surv<span class="hljs-punctuation">(</span>df<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>f1 <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../fig.3/B_ref_A_fiig.3_C/coxph.rds&#x27;</span><span class="hljs-punctuation">)</span><br>f1<span class="hljs-operator">$</span>coefficients <span class="hljs-operator">&lt;-</span> Ridge.cf<span class="hljs-punctuation">[</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>f1<span class="hljs-operator">$</span>coefficients<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;coef&#x27;</span><span class="hljs-punctuation">]</span><br>tmp_dat <span class="hljs-operator">&lt;-</span> f_COXPH_predict<span class="hljs-punctuation">(</span>all_sets<span class="hljs-punctuation">,</span> f1<span class="hljs-punctuation">)</span><br>tmp_surv <span class="hljs-operator">&lt;-</span> f_surv_list<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> tau <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>timeROC<span class="hljs-punctuation">)</span><br>f_timeROC_one <span class="hljs-operator">&lt;-</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">,</span> geneN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    years2 <span class="hljs-operator">&lt;-</span> timeROC<span class="hljs-punctuation">(</span><span class="hljs-built_in">T</span><span class="hljs-operator">=</span>dat<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span>delta<span class="hljs-operator">=</span>dat<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><br>                          marker<span class="hljs-operator">=</span>dat<span class="hljs-punctuation">[[</span>geneN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>cause<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>                          weighting<span class="hljs-operator">=</span><span class="hljs-string">&quot;marginal&quot;</span><span class="hljs-punctuation">,</span><br>        <span class="hljs-comment">#                   other_markers=as.matrix(df$`1-year`),</span><br>                          times<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ROC<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> iid<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    auc2.ci <span class="hljs-operator">&lt;-</span> confint<span class="hljs-punctuation">(</span>years2<span class="hljs-punctuation">,</span> parm<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> level <span class="hljs-operator">=</span> <span class="hljs-number">0.95</span><span class="hljs-punctuation">,</span>n.sim<span class="hljs-operator">=</span><span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>    auc2.ci <span class="hljs-operator">&lt;-</span> auc2.ci<span class="hljs-operator">$</span>CI_AUC<br>    auc2.ci<br>    years2.auc1 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br>    years2.auc2 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</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-string">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br>    years2.auc3 <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>years2<span class="hljs-operator">$</span>AUC<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span><span class="hljs-number">100</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</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-string">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>auc2.ci<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;)%&#x27;</span><span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>roc<span class="hljs-operator">=</span>years2<span class="hljs-punctuation">,</span> auc1<span class="hljs-operator">=</span>years2.auc1<span class="hljs-punctuation">,</span> auc2<span class="hljs-operator">=</span>years2.auc2<span class="hljs-punctuation">,</span> auc3<span class="hljs-operator">=</span>years2.auc3<span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> f_timeROC_one<span class="hljs-punctuation">(</span>tmp_dat<span class="hljs-operator">$</span>GSE54460<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Risk_Score&#x27;</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> ylim<span class="hljs-operator">=</span><span class="hljs-built_in">c</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> xlim<span class="hljs-operator">=</span><span class="hljs-built_in">c</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> main<span class="hljs-operator">=</span><span class="hljs-string">&quot;Time dependent ROC of Risk_Score in train_data&quot;</span><span class="hljs-punctuation">,</span> xlab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;1-Specificity&#x27;</span><span class="hljs-punctuation">,</span> ylab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Sensitivity&#x27;</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>roc<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">,</span> lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span>      <br>plot<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>roc<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">)</span> <br>plot<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>roc<span class="hljs-punctuation">,</span>time<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>add<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span><span class="hljs-string">&quot;#E18727FF&quot;</span><span class="hljs-punctuation">)</span> <br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;bottomright&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 1-year =&quot;</span><span class="hljs-punctuation">,</span>tmp<span class="hljs-operator">$</span>auc1<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 3-year =&quot;</span><span class="hljs-punctuation">,</span>tmp<span class="hljs-operator">$</span>auc2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                 paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;AUC of 5-year =&quot;</span><span class="hljs-punctuation">,</span>tmp<span class="hljs-operator">$</span>auc3<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>       col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#BC3C29FF&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#0072B5FF&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#E18727FF&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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