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            <h1 id="seo-header">clusterProfiler：构建Disease Ontology数据库</h1>
            
            
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                <p>与常用的基因功能注释数据库类似，<a target="_blank" rel="noopener" href="https://disease-ontology.org/">Disease Ontolog</a>通过参照MeSH, ICD等疾病分类标准，对人类的常见疾病与罕见病进行了归纳整理，提供了一个统一的，标准化的疾病分类系统。</p>
<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/2126.html">conda activate clusterprofiler</a></li>
<li>conda install -c bioconda bioconductor-biomart -y</li>
</ul>
<h2 id="获得基础数据"><a href="#获得基础数据" class="headerlink" title="获得基础数据"></a>获得基础数据</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><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs R">tmp <span class="hljs-operator">&lt;-</span> DOSE<span class="hljs-operator">:::</span>get_DO_data<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;DO&#x27;</span><span class="hljs-punctuation">)</span><br>DO <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>DO<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>PATHID2NAME<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>DO<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;name&#x27;</span><br>DO<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;gsid&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>DO<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>DO<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>DO<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> DO<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">[</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><span class="hljs-punctuation">]</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>PATHID <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-operator">$</span>PATHID2EXTID<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    line <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>PATHID2EXTID<span class="hljs-punctuation">[[</span>PATHID<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> PATHID<span class="hljs-punctuation">,</span> times <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><br>    DO<span class="hljs-operator">$</span>TERM2GENE <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>DO<span class="hljs-operator">$</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-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>colnames<span class="hljs-punctuation">(</span>DO<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></code></pre></td></tr></table></figure>

<h2 id="转化ENTREZID"><a href="#转化ENTREZID" class="headerlink" title="转化ENTREZID"></a>转化ENTREZID</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">tmp <span class="hljs-operator">&lt;-</span> AnnotationDbi<span class="hljs-operator">::</span>select<span class="hljs-punctuation">(</span>org.Hs.eg.db<span class="hljs-operator">::</span>org.Hs.eg.db<span class="hljs-punctuation">,</span>keys<span class="hljs-operator">=</span>DO<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-operator">$</span>gene<span class="hljs-punctuation">,</span>columns<span class="hljs-operator">=</span><span class="hljs-string">&#x27;SYMBOL&#x27;</span><span class="hljs-punctuation">,</span> keytype<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENTREZID&#x27;</span><span class="hljs-punctuation">)</span><br>DO<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-operator">$</span>gene <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>SYMBOL<br>DO<span class="hljs-operator">$</span>TERM2GENE <span class="hljs-operator">&lt;-</span> na.omit<span class="hljs-punctuation">(</span>DO<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>DO<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;DO.hsa.rds&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># tmp[is.na(tmp$SYMBOL),]</span><br><span class="hljs-comment"># library(biomaRt)</span><br><span class="hljs-comment"># listMarts() #看看有多少数据库资源</span><br><span class="hljs-comment"># ensembl=useMart(&quot;ensembl&quot;)</span><br><span class="hljs-comment"># listDatasets(ensembl)#看看选择的数据库里面有多少数据表，这个跟物种相关</span><br><span class="hljs-comment"># ensembl = useDataset(&quot;hsapiens_gene_ensembl&quot;,mart=ensembl)</span><br><span class="hljs-comment"># ensembl = useMart(&quot;ensembl&quot;,dataset=&quot;hsapiens_gene_ensembl&quot;) # 这是一步法选择人类的ensembl数据库代码</span><br><span class="hljs-comment"># searchFilters(mart = ensembl, &#x27;entrezid&#x27;)</span><br><span class="hljs-comment"># getBM(attributes=c(&#x27;hgnc_symbol&#x27;), filters = &#x27;entrezgene_id&#x27;, values = c(&#x27;100128356&#x27;, &#x27;4590&#x27;), mart = ensembl)</span><br></code></pre></td></tr></table></figure>
                
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