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            <h1 id="seo-header">整合多个DEGs</h1>
            
            
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                <h2 id="第一步-读入数据"><a href="#第一步-读入数据" class="headerlink" title="第一步 读入数据"></a>第一步 读入数据</h2><figure class="highlight clean"><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></pre></td><td class="code"><pre><code class="hljs clean"># 配置数据路径<br>root_path = <span class="hljs-string">&quot;~/zlliu/R_data/TCGA&quot;</span><br> <br># 配置结果保存路径<br>output_path = root_path<br><span class="hljs-keyword">if</span> (!file.exists(output_path))&#123;dir.create(output_path)&#125;<br> <br># 设置工作目录，输出文件将保存在此目录下<br>setwd(output_path)<br>getwd()<br><br>su.d &lt;- subset(read.csv(<span class="hljs-string">&#x27;seurat.csv&#x27;</span>), cluster==<span class="hljs-string">&#x27;CRPC&#x27;</span>)<br>su.f &lt;- <span class="hljs-keyword">with</span>(su.d, mean(abs(avg_log2FC)))<br>rownames(su.d) &lt;- su.d$X<br>tcga &lt;- readRDS(<span class="hljs-string">&#x27;tcga.rds&#x27;</span>)<br>gse &lt;- readRDS(<span class="hljs-string">&#x27;gse.rds&#x27;</span>)<br><br></code></pre></td></tr></table></figure>

<h2 id="第二步-规范数据"><a href="#第二步-规范数据" class="headerlink" title="第二步 规范数据"></a>第二步 规范数据</h2><figure class="highlight nginx"><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></pre></td><td class="code"><pre><code class="hljs nginx"><span class="hljs-attribute">degs</span> = list()<br><br>degs<span class="hljs-variable">$scRNA</span> &lt;- su.d[,c(<span class="hljs-string">&#x27;avg_log2FC&#x27;</span>,<span class="hljs-string">&#x27;p_val_adj&#x27;</span>,<span class="hljs-string">&#x27;pct.1&#x27;</span>)]<br>colnames(degs<span class="hljs-variable">$scRNA</span>) &lt;- c(<span class="hljs-string">&#x27;logFC&#x27;</span>,<span class="hljs-string">&#x27;q&#x27;</span>,<span class="hljs-string">&#x27;m&#x27;</span>)<br><br>degs<span class="hljs-variable">$tcga</span> &lt;- tcga<span class="hljs-variable">$deg</span>[,c(<span class="hljs-string">&#x27;log2FoldChange&#x27;</span>,<span class="hljs-string">&#x27;padj&#x27;</span>,<span class="hljs-string">&#x27;baseMean&#x27;</span>)]<br>colnames(degs<span class="hljs-variable">$tcga</span>) &lt;- c(<span class="hljs-string">&#x27;logFC&#x27;</span>,<span class="hljs-string">&#x27;q&#x27;</span>,<span class="hljs-string">&#x27;m&#x27;</span>)<br>degs<span class="hljs-variable">$tcga</span><span class="hljs-variable">$logFC</span> &lt;- -degs<span class="hljs-variable">$tcga</span><span class="hljs-variable">$logFC</span> <span class="hljs-comment"># 转到PRAD为对照</span><br>degs<span class="hljs-variable">$tcga</span><span class="hljs-variable">$m</span> &lt;- log2(degs<span class="hljs-variable">$tcga</span><span class="hljs-variable">$m</span>) <span class="hljs-comment"># 取对数</span><br><br>degs<span class="hljs-variable">$geo</span> &lt;- gse<span class="hljs-variable">$deg</span>[,c(<span class="hljs-string">&#x27;logFC&#x27;</span>, <span class="hljs-string">&#x27;adj.P.Val&#x27;</span>, <span class="hljs-string">&#x27;AveExpr&#x27;</span>)]<br>colnames(degs<span class="hljs-variable">$geo</span>) &lt;- c(<span class="hljs-string">&#x27;logFC&#x27;</span>,<span class="hljs-string">&#x27;q&#x27;</span>,<span class="hljs-string">&#x27;m&#x27;</span>)<br><br></code></pre></td></tr></table></figure>

<h2 id="第三步-整合数据"><a href="#第三步-整合数据" class="headerlink" title="第三步 整合数据"></a>第三步 整合数据</h2><figure class="highlight stylus"><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 stylus">degs<span class="hljs-selector-class">.u</span> &lt;- <span class="hljs-built_in">list</span>()<br>degs<span class="hljs-selector-class">.d</span> &lt;- <span class="hljs-built_in">list</span>()<br><br>degs.u<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$scRNA</span>, logFC &gt; <span class="hljs-number">0</span>)<br>degs.d<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$scRNA</span>, logFC &lt; <span class="hljs-number">0</span>)<br><br>degs.u<span class="hljs-variable">$tcga</span> &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$tcga</span>, logFC &gt; <span class="hljs-number">0</span>)<br>degs.d<span class="hljs-variable">$tcga</span> &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$tcga</span>, logFC &lt; <span class="hljs-number">0</span>)<br><br>degs.u<span class="hljs-variable">$geo</span>  &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$geo</span> , logFC &gt; <span class="hljs-number">0</span>)<br>degs.d<span class="hljs-variable">$geo</span>  &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$geo</span> , logFC &lt; <span class="hljs-number">0</span>)<br><br>degs<span class="hljs-selector-class">.fm</span> &lt;- <span class="hljs-built_in">list</span>()<br>degs<span class="hljs-selector-class">.ffc</span> &lt;- <span class="hljs-built_in">list</span>()<br><br>degs.fm<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$scRNA</span>, <span class="hljs-built_in">mean</span>(m) - <span class="hljs-number">2</span>*<span class="hljs-built_in">sd</span>(m))<br>degs.fm<span class="hljs-variable">$tcga</span> &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$tcga</span>, <span class="hljs-built_in">mean</span>(m)- <span class="hljs-number">3</span>*<span class="hljs-built_in">sd</span>(m))<br>degs.fm<span class="hljs-variable">$geo</span> &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$geo</span>, <span class="hljs-built_in">mean</span>(m)- <span class="hljs-number">4</span>*<span class="hljs-built_in">sd</span>(m))<br><br>degs.ffc<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$scRNA</span>, <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(logFC)) + <span class="hljs-number">0</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(logFC)))<br>degs.ffc<span class="hljs-variable">$tcga</span> &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$tcga</span>, <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(logFC)) + <span class="hljs-number">0</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(logFC)))<br>degs.ffc<span class="hljs-variable">$geo</span>  &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$geo</span> , <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(logFC)) + <span class="hljs-number">0</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(logFC)))<br>degs.ffc<span class="hljs-variable">$lo</span>  &lt;- <span class="hljs-built_in">with</span>(degs<span class="hljs-variable">$lo</span> , <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(logFC)) + <span class="hljs-number">1</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(logFC)))<br><br>degs<span class="hljs-selector-class">.lo</span> &lt;- <span class="hljs-built_in">subset</span>(degs<span class="hljs-variable">$lo</span>, <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$lo</span> &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.u<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">subset</span>(degs.u<span class="hljs-variable">$scRNA</span> , <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$scRNA</span> &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.d<span class="hljs-variable">$scRNA</span> &lt;- <span class="hljs-built_in">subset</span>(degs.d<span class="hljs-variable">$scRNA</span>, <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$scRNA</span> &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.u<span class="hljs-variable">$tcga</span>  &lt;- <span class="hljs-built_in">subset</span>(degs.u<span class="hljs-variable">$tcga</span>  , <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$tcga</span>  &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.d<span class="hljs-variable">$tcga</span>  &lt;- <span class="hljs-built_in">subset</span>(degs.d<span class="hljs-variable">$tcga</span> , <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$tcga</span>  &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.u<span class="hljs-variable">$geo</span> &lt;- <span class="hljs-built_in">subset</span>(degs.u<span class="hljs-variable">$geo</span>, <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$geo</span>  &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br>degs.d<span class="hljs-variable">$geo</span> &lt;- <span class="hljs-built_in">subset</span>(degs.d<span class="hljs-variable">$geo</span>, <span class="hljs-built_in">abs</span>(logFC) &gt; degs.ffc<span class="hljs-variable">$geo</span>  &amp; <span class="hljs-selector-tag">q</span> &lt;<span class="hljs-number">0.05</span>)<br><br></code></pre></td></tr></table></figure>

<h2 id="第四步-可视化"><a href="#第四步-可视化" class="headerlink" title="第四步 可视化"></a>第四步 可视化</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>RColorBrewer<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># options(BioC_mirror=&quot;https://mirrors.tuna.tsinghua.edu.cn/bioconductor&quot;)</span><br><span class="hljs-comment"># BiocManager::install(&#x27;ggvenn&#x27;)</span><br>library<span class="hljs-punctuation">(</span>ggvenn<span class="hljs-punctuation">)</span><br>col_Paired <span class="hljs-operator">&lt;-</span> colorRampPalette<span class="hljs-punctuation">(</span>brewer.pal<span class="hljs-punctuation">(</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Paired&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_venn <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">,</span> lc_c<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><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>lc_c<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>lc_c <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    lc_col <span class="hljs-operator">&lt;-</span> col_Paired<span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    ggvenn<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">,</span>lc_c<span class="hljs-punctuation">,</span> show_percentage <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br>       stroke_color <span class="hljs-operator">=</span> <span class="hljs-string">&quot;white&quot;</span><span class="hljs-punctuation">,</span><br>       fill_color <span class="hljs-operator">=</span> lc_col<span class="hljs-punctuation">,</span><br>       set_name_color <span class="hljs-operator">=</span> lc_col<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight stylus"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs stylus"><span class="hljs-function"><span class="hljs-title">f_venn</span><span class="hljs-params">(u)</span></span><br><span class="hljs-function"><span class="hljs-title">f_venn</span><span class="hljs-params">(d)</span></span><br></code></pre></td></tr></table></figure>
                
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