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            <h1 id="seo-header">有序分类Logistic回归</h1>
            
            
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                <h2 id="Logistic回归的假设"><a href="#Logistic回归的假设" class="headerlink" title="Logistic回归的假设"></a>Logistic回归的假设</h2><ul>
<li><strong>假设1</strong>：因变量唯一，且为有序多分类变量</li>
<li><strong>假设2</strong>：存在一个或多个自变量，可为连续、有序多分类或无序分类变量。</li>
<li><strong>假设3</strong>：自变量之间无多重共线性。</li>
<li><strong>假设4</strong>：模型满足“比例优势”假设。</li>
</ul>
<h2 id="通过conda安装纯净环境的Logistic分析包"><a href="#通过conda安装纯净环境的Logistic分析包" class="headerlink" title="通过conda安装纯净环境的Logistic分析包"></a>通过conda安装纯净环境的Logistic分析包</h2><ul>
<li>conda create -n logistic -c conda-forge r-base&#x3D;4.1.3</li>
<li>conda activate logistic</li>
<li>conda install -c conda-forge r-tidyverse&#x3D;1.3.1 -y</li>
<li>conda install -c conda-forge r-irkernel -y</li>
<li>conda install -c conda-forge r-foreign -y</li>
<li>conda install -c conda-forge r-mass -y</li>
<li>conda install -c conda-forge r-hmisc -y</li>
<li>conda install -c conda-forge r-reshape2 -y</li>
<li>conda install -c r r-car -y</li>
<li>Rscript -e “IRkernel::installspec(name&#x3D;’logistic’, displayname&#x3D;’r-logistic’)”</li>
</ul>
<h2 id="准备数据"><a href="#准备数据" class="headerlink" title="准备数据"></a>准备数据</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs R">group <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;prad_tpm_Cu_death.rds&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>clinical <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;TCGA-PRAD_clinical.csv&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;bcr_patient_barcode&#x27;</span><span class="hljs-punctuation">)</span><br>f_TCGA_gleason_grade <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>primary_gleason_grade<span class="hljs-punctuation">,</span> secondary_gleason_grade<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    primary_gleason_grade <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>data.frame<span class="hljs-punctuation">(</span>strsplit<span class="hljs-punctuation">(</span>primary_gleason_grade<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; &#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</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-punctuation">)</span><span class="hljs-punctuation">)</span><br>    secondary_gleason_grade <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>data.frame<span class="hljs-punctuation">(</span>strsplit<span class="hljs-punctuation">(</span>secondary_gleason_grade<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; &#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</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-punctuation">)</span><span class="hljs-punctuation">)</span><br>    primary_gleason_grade <span class="hljs-operator">+</span> secondary_gleason_grade<br><span class="hljs-punctuation">&#125;</span><br>clinical<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;gleason&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> f_TCGA_gleason_grade<span class="hljs-punctuation">(</span>clinical<span class="hljs-operator">$</span>primary_gleason_grade<span class="hljs-punctuation">,</span> clinical<span class="hljs-operator">$</span>secondary_gleason_grade<span class="hljs-punctuation">)</span><br>mergeID <span class="hljs-operator">&lt;-</span> intersect<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>clinical<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> rownames<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">[</span>mergeID<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> clinical<span class="hljs-punctuation">[</span>mergeID<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gleason&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;dcf_time&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;dcf_status&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;os_time&#x27;</span><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-punctuation">)</span><br>df<span class="hljs-punctuation">[</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> ifelse<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[</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><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><br>df<br></code></pre></td></tr></table></figure>

<h2 id="多重共线性检测"><a href="#多重共线性检测" class="headerlink" title="多重共线性检测"></a>多重共线性检测</h2><ul>
<li>qr(as.matrix(df[1:10]))$rank &#x3D;&#x3D; 10</li>
<li>kappa(cor(as.matrix(df[1:10])), exact&#x3D; TRUE) &lt; 100</li>
<li>library(car)</li>
<li>vif(lm.sol)</li>
</ul>
<h2 id="Logistic回归"><a href="#Logistic回归" class="headerlink" title="Logistic回归"></a>Logistic回归</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></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>foreign<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>MASS<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>Hmisc<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>reshape2<span class="hljs-punctuation">)</span><br>lmf <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;factor(gleason)~&quot;</span><span class="hljs-punctuation">,</span> paste<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-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">10</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>lmf<br>m <span class="hljs-operator">&lt;-</span> polr<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>lmf<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> df<span class="hljs-punctuation">,</span> Hess <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>m<br>drop1<span class="hljs-punctuation">(</span>m<span class="hljs-punctuation">,</span>test<span class="hljs-operator">=</span><span class="hljs-string">&quot;Chi&quot;</span><span class="hljs-punctuation">)</span> <br><span class="hljs-punctuation">(</span>ci <span class="hljs-operator">&lt;-</span> confint<span class="hljs-punctuation">(</span>m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">exp</span><span class="hljs-punctuation">(</span>cbind<span class="hljs-punctuation">(</span>OR <span class="hljs-operator">=</span> coef<span class="hljs-punctuation">(</span>m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ci<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span><span class="hljs-built_in">exp</span><span class="hljs-punctuation">(</span>cbind<span class="hljs-punctuation">(</span>OR <span class="hljs-operator">=</span> coef<span class="hljs-punctuation">(</span>m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ci<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</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> drop1<span class="hljs-punctuation">(</span>m<span class="hljs-punctuation">,</span>test<span class="hljs-operator">=</span><span class="hljs-string">&quot;Chi&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pr(&gt;Chi)&#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>colnames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">3</span><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<br>saveRDS<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Logistic.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="绘制森林图"><a href="#绘制森林图" class="headerlink" title="绘制森林图"></a>绘制森林图</h2><p><a target="_blank" rel="noopener" href="https://occdn.limour.top/2097.html">绘制函数来源</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></pre></td><td class="code"><pre><code class="hljs R">df <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Logistic.rds&#x27;</span><span class="hljs-punctuation">)</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">6</span><span class="hljs-punctuation">)</span><br>f_forestplot<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> zero <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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