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            <h1 id="seo-header">clusterProfiler：构建MsigDB的数据库</h1>
            
            
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                <p><a href="https://occdn.limour.top/2128.html">clusterProfiler：自定义数据库</a>中展示过构建<a target="_blank" rel="noopener" href="http://www.gsea-msigdb.org/gsea/downloads.jsp">HALLMARKS</a>的方式，但是速度有点慢，这里简单改动一下，对<a target="_blank" rel="noopener" href="https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp#C5">C5_HPO</a>进行构建。</p>
<h2 id="构建"><a href="#构建" class="headerlink" title="构建"></a>构建</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></pre></td><td class="code"><pre><code class="hljs R">text <span class="hljs-operator">&lt;-</span> readLines<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;c5.hpo.v7.5.1.symbols.gmt&quot;</span><span class="hljs-punctuation">,</span> encoding <span class="hljs-operator">=</span> <span class="hljs-string">&quot;UTF-8&quot;</span><span class="hljs-punctuation">)</span><br>text <span class="hljs-operator">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\t&quot;</span><span class="hljs-punctuation">)</span><br>H.ALL <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>TERM2GENE<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> TERM2NAME<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    line <span class="hljs-operator">&lt;-</span> text<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    gsid <span class="hljs-operator">&lt;-</span> line<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    H.ALL<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>i<span class="hljs-punctuation">,</span>gsid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    lc_gsid <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> i<span class="hljs-punctuation">,</span> times <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    H.ALL<span class="hljs-operator">$</span>TERM2GENE <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">,</span> cbind<span class="hljs-punctuation">(</span>lc_gsid<span class="hljs-punctuation">,</span>line<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>colnames<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;name&#x27;</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2GENE<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;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;gene&#x27;</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;C5.HPO.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="富集"><a href="#富集" class="headerlink" title="富集"></a>富集</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">require<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>enrichplot<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>DOSE<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>clusterProfiler<span class="hljs-punctuation">)</span><br>f_kegg_p <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>keggr2<span class="hljs-punctuation">,</span> n <span class="hljs-operator">=</span> <span class="hljs-number">15</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    keggr <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>keggr2<span class="hljs-operator">@</span>result<span class="hljs-punctuation">,</span> p.adjust <span class="hljs-operator">&lt;</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">)</span><br>    keggr<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;-log(Padj)&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-operator">-</span>log10<span class="hljs-punctuation">(</span>keggr<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;p.adjust&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    keggr<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;geneRatio&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> parse_ratio<span class="hljs-punctuation">(</span>keggr<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;GeneRatio&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    keggr<span class="hljs-operator">$</span>Description <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span>keggr<span class="hljs-operator">$</span>Description<span class="hljs-punctuation">,</span> <br>                                       levels<span class="hljs-operator">=</span>keggr<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>keggr<span class="hljs-operator">$</span>geneRatio<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>Description<span class="hljs-punctuation">)</span><br>    ggplot<span class="hljs-punctuation">(</span>head<span class="hljs-punctuation">(</span>keggr<span class="hljs-punctuation">,</span>n<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>geneRatio<span class="hljs-punctuation">,</span>y<span class="hljs-operator">=</span>Description<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><br>        geom_point<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>color<span class="hljs-operator">=</span>`-log(Padj)`<span class="hljs-punctuation">,</span><br>                 size<span class="hljs-operator">=</span>`Count`<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><br>        theme_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><br>        scale_color_gradient<span class="hljs-punctuation">(</span>low<span class="hljs-operator">=</span><span class="hljs-string">&quot;blue1&quot;</span><span class="hljs-punctuation">,</span>high<span class="hljs-operator">=</span><span class="hljs-string">&quot;brown1&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><br>        labs<span class="hljs-punctuation">(</span>y<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br>        theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>angle<span class="hljs-operator">=</span><span class="hljs-number">90</span><span class="hljs-punctuation">,</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span>vjust<span class="hljs-operator">=</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span> size <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>             axis.text.y<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>size <span class="hljs-operator">=</span> <span class="hljs-number">15</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><br>     scale_size<span class="hljs-punctuation">(</span><span class="hljs-built_in">range</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span><span class="hljs-number">10</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br>     theme<span class="hljs-punctuation">(</span>axis.text<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>axis.title<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br>     scale_y_discrete<span class="hljs-punctuation">(</span>labels<span class="hljs-operator">=</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>str_wrap<span class="hljs-punctuation">(</span>gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;_&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; &#x27;</span><span class="hljs-punctuation">,</span> y<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>width <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_title <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>gp<span class="hljs-punctuation">,</span>title<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    gp <span class="hljs-operator">+</span> labs<span class="hljs-punctuation">(</span>title <span class="hljs-operator">=</span> title<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<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></pre></td><td class="code"><pre><code class="hljs R">KEGG <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../MsigDB/C5.HPO.rds&#x27;</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>res <span class="hljs-operator">&lt;-</span> enricher<span class="hljs-punctuation">(</span>gene <span class="hljs-operator">=</span> DEGPH<span class="hljs-operator">$</span>Name<span class="hljs-punctuation">,</span> <br>             pAdjustMethod <span class="hljs-operator">=</span> <span class="hljs-string">&quot;fdr&quot;</span><span class="hljs-punctuation">,</span><br>             pvalueCutoff <span class="hljs-operator">=</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span><br>             qvalueCutoff <span class="hljs-operator">=</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span><br>             TERM2GENE <span class="hljs-operator">=</span> KEGG<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">,</span><br>             TERM2NAME <span class="hljs-operator">=</span> KEGG<span class="hljs-operator">$</span>TERM2NAME<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">12</span><span class="hljs-punctuation">)</span><br>f_kegg_p<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> n <span class="hljs-operator">=</span><span class="hljs-number">15</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_title<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;C42vsLNCaP_EtOH_C5_HPO&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<p><a href="https://occdn.limour.top/2142.html">GSEA以及其他高级绘图</a>，注：GESA添加<code>nPermSimple = 100000</code>可以提高P值计算准确性</p>
<h2 id="通过预分配的方式进行构建"><a href="#通过预分配的方式进行构建" class="headerlink" title="通过预分配的方式进行构建"></a>通过预分配的方式进行构建</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></pre></td><td class="code"><pre><code class="hljs R">text <span class="hljs-operator">&lt;-</span> readLines<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;c5.all.v7.5.1.symbols.gmt&quot;</span><span class="hljs-punctuation">,</span> encoding <span class="hljs-operator">=</span> <span class="hljs-string">&quot;UTF-8&quot;</span><span class="hljs-punctuation">)</span><br>text <span class="hljs-operator">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\t&quot;</span><span class="hljs-punctuation">)</span><br>pre_len <span class="hljs-operator">&lt;-</span> 0<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>line <span class="hljs-operator">&lt;-</span> text<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    pre_len <span class="hljs-operator">&lt;-</span> pre_len <span class="hljs-operator">+</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>H.ALL <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>TERM2NAME<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> TERM2GENE<span class="hljs-operator">=</span>data.frame<span class="hljs-punctuation">(</span>gsid<span class="hljs-operator">=</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span>pre_len<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> gene<span class="hljs-operator">=</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span>pre_len<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>pre_tmp <span class="hljs-operator">&lt;-</span> 0<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>text<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    line <span class="hljs-operator">&lt;-</span> text<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    gsid <span class="hljs-operator">&lt;-</span> line<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    H.ALL<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>i<span class="hljs-punctuation">,</span>gsid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    pre_genelen <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br>    lc_gsid <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> i<span class="hljs-punctuation">,</span> times <span class="hljs-operator">=</span> pre_genelen<span class="hljs-punctuation">)</span><br>    H.ALL<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">[</span><span class="hljs-punctuation">(</span>pre_tmp<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-operator">:</span><span class="hljs-punctuation">(</span>pre_tmp <span class="hljs-operator">+</span> pre_genelen<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>lc_gsid<span class="hljs-punctuation">,</span>line<span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>line<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    pre_tmp <span class="hljs-operator">&lt;-</span> pre_tmp <span class="hljs-operator">+</span> pre_genelen<br><span class="hljs-punctuation">&#125;</span><br>colnames<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2NAME<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;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;name&#x27;</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-operator">$</span>TERM2GENE<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;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;gene&#x27;</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>H.ALL<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;C5.all.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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    var res = [];
    for (var item of el) {
      res.push('.markdown-body > ' + item.trim());
    }
    if (CONFIG.anchorjs.placement === 'left') {
      window.anchors.options.class = 'anchorjs-link-left';
    }
    window.anchors.add(res.join(', '));

    Fluid.events.registerRefreshCallback(function() {
      if ('anchors' in window) {
        anchors.removeAll();
        var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


<script>
  Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    Fluid.plugins.fancyBox();
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
<!-- hexo injector body_end start -->
  <script defer src="/theme-inject/timeliness.js"></script>
<!-- hexo injector body_end end --></body>
</html>