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            <h1 id="seo-header">ReactomePA试用</h1>
            
            
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                <h2 id="安装补充包"><a href="#安装补充包" class="headerlink" title="安装补充包"></a>安装补充包</h2><ul>
<li><a href="https://occdn.limour.top/2275.html">conda activate clusterprofiler</a></li>
<li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</li>
<li>wget -e “https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“ <a target="_blank" rel="noopener" href="https://github.com/YuLab-SMU/ReactomePA/archive/refs/heads/master.zip">https://github.com/YuLab-SMU/ReactomePA/archive/refs/heads/master.zip</a> -O ReactomePA-master.zip</li>
<li>BiocManager::install(“reactome.db”)</li>
<li>devtools::install_local(‘ReactomePA-master.zip’)</li>
</ul>
<h2 id="读入数据"><a href="#读入数据" class="headerlink" title="读入数据"></a>读入数据</h2><p><a href="https://occdn.limour.top/2132.html">差异基因分析</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><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">library<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br>DEG <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;DEG.rds&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-operator">!</span>grepl<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pseudogene&#x27;</span><span class="hljs-punctuation">,</span> gene_type<span class="hljs-punctuation">)</span> <span class="hljs-operator">&amp;</span> baseMean <span class="hljs-operator">&gt;</span> quantile<span class="hljs-punctuation">(</span>baseMean<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;25%&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&amp;</span> padj <span class="hljs-operator">&lt;</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>DEG<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>str_split<span class="hljs-punctuation">(</span>DEG<span class="hljs-operator">$</span>gene_id<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;\\.&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>allEntrez <span class="hljs-operator">=</span> clusterProfiler<span class="hljs-operator">::</span>bitr<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>DEG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> fromType<span class="hljs-operator">=</span><span class="hljs-string">&quot;ENSEMBL&quot;</span><span class="hljs-punctuation">,</span> toType<span class="hljs-operator">=</span><span class="hljs-string">&quot;ENTREZID&quot;</span><span class="hljs-punctuation">,</span> OrgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br>DEG<span class="hljs-operator">$</span>ENSEMBL <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>DEG<span class="hljs-punctuation">)</span><br>lfc <span class="hljs-operator">&lt;-</span> merge<span class="hljs-punctuation">(</span>data.frame<span class="hljs-punctuation">(</span>DEG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> allEntrez<span class="hljs-punctuation">,</span> by<span class="hljs-operator">=</span><span class="hljs-string">&quot;ENSEMBL&quot;</span><span class="hljs-punctuation">)</span><br>lfc <span class="hljs-operator">&lt;-</span> lfc<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>lfc<span class="hljs-operator">$</span>log2FoldChange<span class="hljs-punctuation">,</span> decreasing<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>geneList <span class="hljs-operator">&lt;-</span> lfc<span class="hljs-operator">$</span>log2FoldChange<br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>geneList<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> lfc<span class="hljs-operator">$</span>ENTREZID<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></pre></td><td class="code"><pre><code class="hljs R">x <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;DEG_filer.rds&#x27;</span><span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>str_split<span class="hljs-punctuation">(</span>x<span class="hljs-operator">$</span>gene_id<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;\\.&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>cand.entrez <span class="hljs-operator">=</span> clusterProfiler<span class="hljs-operator">::</span>bitr<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> fromType<span class="hljs-operator">=</span><span class="hljs-string">&quot;ENSEMBL&quot;</span><span class="hljs-punctuation">,</span> toType<span class="hljs-operator">=</span><span class="hljs-string">&quot;ENTREZID&quot;</span><span class="hljs-punctuation">,</span> OrgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>ENTREZID<br></code></pre></td></tr></table></figure>

<h2 id="进行分析"><a href="#进行分析" class="headerlink" title="进行分析"></a>进行分析</h2><h3 id="ORA"><a href="#ORA" class="headerlink" title="ORA"></a>ORA</h3><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></pre></td><td class="code"><pre><code class="hljs R">set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">123</span><span class="hljs-punctuation">)</span><br>pway <span class="hljs-operator">=</span> ReactomePA<span class="hljs-operator">::</span>enrichPathway<span class="hljs-punctuation">(</span>gene <span class="hljs-operator">=</span> cand.entrez<span class="hljs-punctuation">)</span><br>pway <span class="hljs-operator">=</span> clusterProfiler<span class="hljs-operator">::</span>setReadable<span class="hljs-punctuation">(</span>pway<span class="hljs-punctuation">,</span> OrgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br>pway <span class="hljs-operator">=</span> enrichplot<span class="hljs-operator">::</span>pairwise_termsim<span class="hljs-punctuation">(</span>pway<span class="hljs-punctuation">)</span><br>pway<span class="hljs-operator">@</span>result<br></code></pre></td></tr></table></figure>

<h3 id="GSEA"><a href="#GSEA" class="headerlink" title="GSEA"></a>GSEA</h3><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></pre></td><td class="code"><pre><code class="hljs R">set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">123</span><span class="hljs-punctuation">)</span><br>pwayGSE <span class="hljs-operator">&lt;-</span> ReactomePA<span class="hljs-operator">::</span>gsePathway<span class="hljs-punctuation">(</span>geneList<span class="hljs-punctuation">,</span> eps <span class="hljs-operator">=</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>pwayGSE <span class="hljs-operator">=</span> clusterProfiler<span class="hljs-operator">::</span>setReadable<span class="hljs-punctuation">(</span>pwayGSE<span class="hljs-punctuation">,</span> OrgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br>pwayGSE <span class="hljs-operator">=</span> enrichplot<span class="hljs-operator">::</span>pairwise_termsim<span class="hljs-punctuation">(</span>pwayGSE<span class="hljs-punctuation">)</span><br>pwayGSE<span class="hljs-operator">@</span>result<br></code></pre></td></tr></table></figure>
                
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