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            <h1 id="seo-header">COXPH的变量筛选</h1>
            
            
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                <p>返工的血泪教训，单因素COXPH做完显著是不够的，此时应该再来一次多因素COXPH，剔除那些不具有独立预后能力的变量。</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><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></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">$</span>coefficients<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pr(&gt;z)&#x27;</span><span class="hljs-punctuation">]</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;VarName&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_DEG_coxph_GeneList <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">,</span> geneNs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>geneNs<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>f_DEG_coxph_oneGene<span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">,</span>geneNs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    y <span class="hljs-operator">&lt;-</span> Surv<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>dat<span class="hljs-operator">$</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">$</span>pfs_status <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    y <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><br>    x <span class="hljs-operator">&lt;-</span> dat<span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>geneNs<span class="hljs-punctuation">]</span><br>    x <span class="hljs-operator">&lt;-</span> as.matrix<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><br>    df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span>y<span class="hljs-punctuation">)</span><br>    df <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>df<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(time, status==1)~&quot;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;`&#x27;</span><span class="hljs-punctuation">,</span>geneNs<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;`&#x27;</span><span class="hljs-punctuation">,</span>sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;+&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</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> FPv<span class="hljs-operator">=</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">,</span> strict<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-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>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>strict<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> Pvalue<span class="hljs-operator">&lt;</span>FPv<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>VarName<br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>data.frame<span class="hljs-punctuation">(</span>mean<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> lower<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> upper<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> Pvalue<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> VarName<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res <span class="hljs-operator">&lt;-</span> f_DEG_coxph_GeneList<span class="hljs-punctuation">(</span>trainSet<span class="hljs-punctuation">,</span> res<span class="hljs-punctuation">)</span><br>    res<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>Pvalue<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><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> FPv<span class="hljs-operator">=</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">,</span> strict<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>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> FPv <span class="hljs-operator">=</span> FPv<span class="hljs-punctuation">,</span> strict <span class="hljs-operator">=</span> strict<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>x <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../A_ref_A_fiig.2_A/hub.rds&#x27;</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>tmp <span class="hljs-operator">&lt;-</span> f_DEG_coxph_Sets<span class="hljs-punctuation">(</span>train_sets<span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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