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  133. <h1 id="seo-header">clusterProfiler:构建WikiPathways数据库</h1>
  134. <div class="markdown-body">
  135. <p><a target="_blank" rel="noopener" href="https://www.wikipathways.org/">WikiPathways</a>是一个开放协作平台,旨在促进生物学界对通路信息的贡献和维护。它提供了一种新的模型,可以增强和补充<a target="_blank" rel="noopener" href="http://www.genome.jp/kegg/">KEGG</a>、<a target="_blank" rel="noopener" href="http://www.reactome.org/">Reactome</a>和<a target="_blank" rel="noopener" href="http://www.pathwaycommons.org/pc/">Pathway Commons</a>等正在进行的工作。</p>
  136. <h2 id="安装相应的R包"><a href="#安装相应的R包" class="headerlink" title="安装相应的R包"></a>安装相应的R包</h2><ul>
  137. <li><a target="_blank" rel="noopener" href="https://occdn.limour.top/2126.htm">conda activate clusterprofiler</a></li>
  138. <li>conda install -c bioconda bioconductor-rwikipathways -y</li>
  139. </ul>
  140. <h2 id="初步建立数据库"><a href="#初步建立数据库" class="headerlink" title="初步建立数据库"></a>初步建立数据库</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></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>rWikiPathways<span class="hljs-punctuation">)</span><br>wp <span class="hljs-operator">&lt;-</span> downloadPathwayArchive<span class="hljs-punctuation">(</span>organism<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Homo sapiens&#x27;</span><span class="hljs-punctuation">,</span> format<span class="hljs-operator">=</span><span class="hljs-string">&#x27;gmt&#x27;</span><span class="hljs-punctuation">)</span><br>text <span class="hljs-operator">&lt;-</span> readLines<span class="hljs-punctuation">(</span>wp<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>WP <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> WP<span class="hljs-operator">$</span>TERM2NAME <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</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> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>k <span class="hljs-keyword">in</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">&#123;</span><br> WP<span class="hljs-operator">$</span>TERM2GENE <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2GENE<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>i<span class="hljs-punctuation">,</span>line<span class="hljs-punctuation">[</span>k<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br>colnames<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</span>TERM2NAME<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;gsid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;name&#x27;</span><span class="hljs-punctuation">)</span><br>colnames<span class="hljs-punctuation">(</span>WP<span class="hljs-operator">$</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>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>WP<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></code></pre></td></tr></table></figure>
  141. <h2 id="修订部分更新"><a href="#修订部分更新" class="headerlink" title="修订部分更新"></a>修订部分更新</h2><ul>
  142. <li>tmp[is.na(tmp$SYMBOL),] 找到所有转换失败的ENTREZID,比如 388813</li>
  143. <li>访问 <a target="_blank" rel="noopener" href="https://www.ncbi.nlm.nih.gov/gene/">https://www.ncbi.nlm.nih.gov/gene/</a><ENTREZID> 得到更新信息</li>
  144. <li>比如 388813 现在已经更名为 64092,HGNC确认其官方SYMBOL为 SAMSN1</li>
  145. <li>tmp[is.na(tmp$SYMBOL), ‘SYMBOL’] &lt;- c(‘SAMSN1’, rep(‘S1PR3’,3)),手动更新信息</li>
  146. <li>WP$TERM2GENE$gene &lt;- tmp$SYMBOL 更改ENTREZID为SYMBOL</li>
  147. <li>saveRDS(WP,’WP.hsa.rds’) 保存数据库</li>
  148. <li>自定义数据库的使用方法见下面的博文</li>
  149. </ul>
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  232. Fluid.utils.waitElementVisible('#waline .vcontent', () => {
  233. var imgSelector = '#waline .vcontent img:not(.vemoji)';
  234. Fluid.plugins.imageCaption(imgSelector);
  235. Fluid.plugins.fancyBox(imgSelector);
  236. })
  237. });
  238. });
  239. </script>
  240. <noscript>Please enable JavaScript to view the comments</noscript>
  241. </article>
  242. </article>
  243. </div>
  244. </div>
  245. </div>
  246. <div class="side-col d-none d-lg-block col-lg-2">
  247. <aside class="sidebar" style="margin-left: -1rem">
  248. <div id="toc">
  249. <p class="toc-header">
  250. <i class="iconfont icon-list"></i>
  251. <span>Table of Contents</span>
  252. </p>
  253. <div class="toc-body" id="toc-body"></div>
  254. </div>
  255. </aside>
  256. </div>
  257. </div>
  258. </div>
  259. <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
  260. <i class="iconfont icon-arrowup" aria-hidden="true"></i>
  261. </a>
  262. <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
  263. aria-hidden="true">
  264. <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
  265. <div class="modal-content">
  266. <div class="modal-header text-center">
  267. <h4 class="modal-title w-100 font-weight-bold">Search</h4>
  268. <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
  269. <span aria-hidden="true">&times;</span>
  270. </button>
  271. </div>
  272. <div class="modal-body mx-3">
  273. <div class="md-form mb-5">
  274. <input type="text" id="local-search-input" class="form-control validate">
  275. <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
  276. </div>
  277. <div class="list-group" id="local-search-result"></div>
  278. </div>
  279. </div>
  280. </div>
  281. </div>
  282. </main>
  283. <footer>
  284. <div class="footer-inner">
  285. <div class="footer-content">
  286. <a target="_blank" rel="nofollow noopener" href="http://www.beian.gov.cn/portal/registerSystemInfo?recordcode=43130202000203"><img src="https://img.limour.top/2023/08/27/64eadeb81d6a0.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload>湘公网安备 43130202000203号 </a> <a target="_blank" rel="nofollow noopener" href="https://beian.miit.gov.cn/">湘ICP备20008299号 </a> <a target="_blank" rel="nofollow noopener" href="https://icp.gov.moe/?keyword=20210128">萌ICP备20210128号</a> <br> <a href="https://www.foreverblog.cn/" target="_blank"> <img src="https://img.foreverblog.cn/logo_en_default.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="" style="width:auto;height:24px"> </a> <br> <a href="https://hexo.io" target="_blank" rel="nofollow noopener"><span>Hexo</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/fluid-dev/hexo-theme-fluid" target="_blank" rel="nofollow noopener"><span>Fluid</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/limour-blog/archives-b" target="_blank" rel="nofollow noopener"><span>SRC</span></a>
  287. </div>
  288. </div>
  289. </footer>
  290. <!-- Scripts -->
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  292. <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
  293. <script>
  294. NProgress.configure({"showSpinner":false,"trickleSpeed":100})
  295. NProgress.start()
  296. window.addEventListener('load', function() {
  297. NProgress.done();
  298. })
  299. </script>
  300. <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
  301. <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
  302. <script src="/js/events.js" ></script>
  303. <script src="/js/plugins.js" ></script>
  304. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  305. <script>
  306. (function (window, document) {
  307. var typing = Fluid.plugins.typing;
  308. var subtitle = document.getElementById('subtitle');
  309. if (!subtitle || !typing) {
  310. return;
  311. }
  312. var text = subtitle.getAttribute('data-typed-text');
  313. typing(text);
  314. })(window, document);
  315. </script>
  316. <script src="/js/img-lazyload.js" ></script>
  317. <script>
  318. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  319. var toc = jQuery('#toc');
  320. if (toc.length === 0 || !window.tocbot) { return; }
  321. var boardCtn = jQuery('#board-ctn');
  322. var boardTop = boardCtn.offset().top;
  323. window.tocbot.init(Object.assign({
  324. tocSelector : '#toc-body',
  325. contentSelector : '.markdown-body',
  326. linkClass : 'tocbot-link',
  327. activeLinkClass : 'tocbot-active-link',
  328. listClass : 'tocbot-list',
  329. isCollapsedClass: 'tocbot-is-collapsed',
  330. collapsibleClass: 'tocbot-is-collapsible',
  331. scrollSmooth : true,
  332. includeTitleTags: true,
  333. headingsOffset : -boardTop,
  334. }, CONFIG.toc));
  335. if (toc.find('.toc-list-item').length > 0) {
  336. toc.css('visibility', 'visible');
  337. }
  338. Fluid.events.registerRefreshCallback(function() {
  339. if ('tocbot' in window) {
  340. tocbot.refresh();
  341. var toc = jQuery('#toc');
  342. if (toc.length === 0 || !tocbot) {
  343. return;
  344. }
  345. if (toc.find('.toc-list-item').length > 0) {
  346. toc.css('visibility', 'visible');
  347. }
  348. }
  349. });
  350. });
  351. </script>
  352. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  353. <script>Fluid.plugins.codeWidget();</script>
  354. <script>
  355. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  356. window.anchors.options = {
  357. placement: CONFIG.anchorjs.placement,
  358. visible : CONFIG.anchorjs.visible
  359. };
  360. if (CONFIG.anchorjs.icon) {
  361. window.anchors.options.icon = CONFIG.anchorjs.icon;
  362. }
  363. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  364. var res = [];
  365. for (var item of el) {
  366. res.push('.markdown-body > ' + item.trim());
  367. }
  368. if (CONFIG.anchorjs.placement === 'left') {
  369. window.anchors.options.class = 'anchorjs-link-left';
  370. }
  371. window.anchors.add(res.join(', '));
  372. Fluid.events.registerRefreshCallback(function() {
  373. if ('anchors' in window) {
  374. anchors.removeAll();
  375. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  376. var res = [];
  377. for (var item of el) {
  378. res.push('.markdown-body > ' + item.trim());
  379. }
  380. if (CONFIG.anchorjs.placement === 'left') {
  381. anchors.options.class = 'anchorjs-link-left';
  382. }
  383. anchors.add(res.join(', '));
  384. }
  385. });
  386. });
  387. </script>
  388. <script>
  389. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  390. Fluid.plugins.fancyBox();
  391. });
  392. </script>
  393. <script>Fluid.plugins.imageCaption();</script>
  394. <script src="/js/local-search.js" ></script>
  395. <!-- 主题的启动项,将它保持在最底部 -->
  396. <!-- the boot of the theme, keep it at the bottom -->
  397. <script src="/js/boot.js" ></script>
  398. <noscript>
  399. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  400. </noscript>
  401. <!-- hexo injector body_end start -->
  402. <script defer src="/theme-inject/timeliness.js"></script>
  403. <!-- hexo injector body_end end --></body>
  404. </html>