{"id":24804,"date":"2024-01-17T10:08:28","date_gmt":"2024-01-17T02:08:28","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24804"},"modified":"2024-01-17T10:08:30","modified_gmt":"2024-01-17T02:08:30","slug":"%e5%9f%ba%e5%9b%a0%e4%b9%8b%e6%97%85%ef%bc%9aclusterprofiler%e6%8f%ad%e7%a4%ba%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90%e4%b8%96%e7%95%8c%e7%9a%84%e5%a5%a5%e7%a7%98%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24804","title":{"rendered":"\u57fa\u56e0\u4e4b\u65c5\uff1aclusterProfiler\u63ed\u793a\u5bcc\u96c6\u5206\u6790\u4e16\u754c\u7684\u5965\u79d8\uff01"},"content":{"rendered":"<p>\u4f60\u77e5\u9053\u5982\u4f55\u4f7f\u7528clusterProfiler\u5bf9DOSE\u5305\u4e2d\u7684\u6570\u636e\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u561b\uff1f\u4eca\u5929\u5c0f\u679c\u5c31\u6765\u6559\u4f60\u8f7b\u677e\u5b8c\u6210\u5bcc\u96c6\u5206\u6790\u7684\u6d41\u7a0b\u5e76\u901a\u8fc7\u4e0d\u540c\u7684R\u5305\u6765\u5b9e\u73b0\u53ef\u89c6\u5316\uff01\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/p>\n<p><strong>\u4e86\u89e3clusterProfiler<\/strong><\/p>\n<p>clusterProfiler\u5305\u662f\u7528\u4e8e\u66f4\u5168\u9762\u548c\u7075\u6d3b\u7684\u57fa\u56e0\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u7684\u5de5\u5177\u3002\u5b83\u63d0\u4f9b\u4e86\u6bd4DOSE\u66f4\u591a\u7684\u529f\u80fd\u548c\u53ef\u5b9a\u5236\u9009\u9879\uff0c\u80fd\u591f\u8fdb\u884c\u66f4\u6df1\u5165\u7684\u529f\u80fd\u89e3\u91ca\u548c\u5206\u6790\u3002<\/p>\n<p>\u4e3b\u8981\u529f\u80fd\u6709\uff1a<\/p>\n<ul>\n<li><strong>\u5bcc\u96c6\u5206\u6790\uff1a<\/strong>clusterProfiler\u5305\u652f\u6301\u591a\u79cd\u751f\u7269\u4fe1\u606f\u5b66\u6570\u636e\u5e93\uff08\u5982GO\u3001KEGG\u3001Reactome\uff09\u63d0\u4f9b\u7684\u6ce8\u91ca\u6570\u636e\uff0c\u53ef\u4ee5\u8fdb\u884c\u66f4\u5e7f\u6cdb\u7684\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u3002<\/li>\n<li><strong>\u53ef\u89c6\u5316\uff1a<\/strong>clusterProfiler\u5305\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u53ef\u89c6\u5316\u529f\u80fd\uff0c\u5305\u62ec\u67f1\u72b6\u56fe\u3001\u6563\u70b9\u56fe\u7b49\uff0c\u7528\u4e8e\u76f4\u89c2\u5c55\u793a\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u6570\u636e\u3002<\/li>\n<li><strong>\u5206\u7c7b\u548c\u805a\u7c7b\uff1a<\/strong>clusterProfiler\u5305\u8fd8\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u5206\u7c7b\u548c\u805a\u7c7b\u529f\u80fd\uff0c\u53ef\u4ee5\u5bf9\u57fa\u56e0\u5217\u8868\u8fdb\u884c\u5206\u7ec4\u548c\u805a\u7c7b\uff0c\u5e76\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u4ee5\u53d1\u73b0\u4e0d\u540c\u57fa\u56e0\u5b50\u96c6\u4e4b\u95f4\u7684\u529f\u80fd\u5dee\u5f02\u548c\u76f8\u4f3c\u6027\u3002<\/li>\n<\/ul>\n<p><strong>\u4ec0\u4e48\u662fDOSE\u5305\uff1f<\/strong><\/p>\n<p>DOSE\u5305\u4e3b\u8981\u7528\u4e8e\u57fa\u56e0\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u5b83\u80fd\u591f\u901a\u8fc7\u6bd4\u8f83\u8f93\u5165\u7684\u57fa\u56e0\u5217\u8868\u4e0e\u5df2\u77e5\u7684\u57fa\u56e0\u529f\u80fd\u6ce8\u91ca\u4fe1\u606f\uff0c\u627e\u51fa\u5728\u7279\u5b9a\u529f\u80fd\u7c7b\u522b\u4e2d\u5bcc\u96c6\u7684\u57fa\u56e0\u3002\u8fd9\u4e9b\u529f\u80fd\u7c7b\u522b\u5305\u62ecGene Ontology (GO)\u6ce8\u91ca\u3001KEGG\u901a\u8def\u3001Reactome\u901a\u8def\u7b49\u3002DOSE\u5305\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\uff0c\u7528\u4e8e\u8ba1\u7b97\u5bcc\u96c6\u5206\u6790\u7684\u7ed3\u679c\uff0c\u5e76\u751f\u6210\u6613\u4e8e\u7406\u89e3\u548c\u53ef\u89c6\u5316\u7684\u7ed3\u679c\u3002<\/p>\n<p>\u4e3b\u8981\u529f\u80fd\u4e3a\uff1a<\/p>\n<ul>\n<li><strong>GO\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff1a<\/strong>DOSE\u5305\u53ef\u4ee5\u6267\u884c\u57fa\u4e8eGene Ontology\u7684\u529f\u80fd\u5bcc\u96c6\u5206\u6790\uff0c\u5305\u62ec\u4e09\u4e2a\u65b9\u9762\u7684\u5bcc\u96c6\uff1a\u751f\u7269\u8fc7\u7a0b\uff08biological process\uff09\u3001\u5206\u5b50\u529f\u80fd\uff08molecular function\uff09\u548c\u7ec6\u80de\u7ec4\u5206\uff08cellular component\uff09\u3002<\/li>\n<li><strong>\u901a\u8def\u5bcc\u96c6\u5206\u6790\uff1a<\/strong>DOSE\u5305\u8fd8\u80fd\u8fdb\u884c\u57fa\u4e8eKEGG\u548cReactome\u901a\u8def\u7684\u5bcc\u96c6\u5206\u6790\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4e86\u89e3\u57fa\u56e0\u5728\u7279\u5b9a\u751f\u7269\u5b66\u8def\u5f84\u4e2d\u7684\u4f5c\u7528\u548c\u76f8\u4e92\u5173\u8054\u3002<\/li>\n<li><strong>\u57fa\u56e0\u96c6\u5408\u6bd4\u8f83\uff1a<\/strong>DOSE\u5305\u53ef\u4ee5\u6bd4\u8f83\u4e0d\u540c\u57fa\u56e0\u96c6\u5408\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u786e\u5b9a\u54ea\u4e9b\u529f\u80fd\u6216\u901a\u8def\u5728\u4e24\u4e2a\u57fa\u56e0\u7ec4\u4e4b\u95f4\u6709\u663e\u8457\u5dee\u5f02\u3002<\/li>\n<\/ul>\n<p><strong>clusterProfiler\u5bcc\u96c6\u5206\u6790<\/strong><\/p>\n<ul>\n<li><strong>\u5b89\u88c5\u4e0e\u5bfc\u5165R\u5305<\/strong><\/li>\n<\/ul>\n<p>\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u5b89\u88c5\u5e76\u52a0\u8f7dDOSE\u548cclusterProfiler\u5305\uff1a<\/p>\n<p>install.packages(&#8220;DOSE&#8221;)<br \/>\ninstall.packages(&#8220;clusterProfiler&#8221;)<\/p>\n<ul>\n<li><strong>\u51c6\u5907\u57fa\u56e0\u6570\u636e<\/strong><\/li>\n<\/ul>\n<p>\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0c\u6211\u4eec\u5c06\u4f7f\u7528DOSE\u5305\u4e2d\u9644\u5e26\u7684geneList\u6570\u636e\u96c6\u54e6\u3002\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u52a0\u8f7d\u6570\u636e\u96c6~<\/p>\n<p>data(geneList, package = &#8220;DOSE&#8221;)<\/p>\n<p>\u7136\u540e\uff0c\u9009\u62e9\u524d100\u4e2a\u57fa\u56e0\u4f5c\u4e3a\u6211\u4eec\u7684\u5206\u6790\u5bf9\u8c61\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"611\" height=\"46\" class=\"wp-image-24805\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-1.png?resize=611%2C46\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-1.png?w=611 611w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-1.png?resize=300%2C23 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-1.png?resize=600%2C45 600w\" sizes=\"(max-width: 611px) 100vw, 611px\" data-recalc-dims=\"1\" \/> g_list &lt;- names(geneList)[1:100]<br \/>\nhead(g_list) # \u67e5\u770b\u9009\u62e9\u7684\u57fa\u56e0\u5217\u8868\u7684\u524d6\u884c<\/p>\n<ul>\n<li><strong>\u5bcc\u96c6\u5206\u6790<\/strong><\/li>\n<\/ul>\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c06\u4f7f\u7528org.Hs.eg.db\u6570\u636e\u5e93\u8fdb\u884c\u529f\u80fd\u5bcc\u96c6\u5206\u6790\u3002\u5927\u5bb6\u4e00\u5b9a\u8981\u786e\u4fdd\u5df2\u5b89\u88c5\u6b64\u6570\u636e\u5e93\uff0c\u7136\u540e\u518d\u52a0\u8f7d\u5b83\u54e6~<\/p>\n<p>library(&#8220;org.Hs.eg.db&#8221;)<\/p>\n<p>\u597d\u5566\uff0c\u73b0\u5728\u6211\u4eec\u53ef\u4ee5\u6211\u4eec\u4f7f\u7528\u4ee5\u4e0b\u4ee3\u7801\u6267\u884cGO\u5bcc\u96c6\u5206\u6790\uff0c\u5e76\u5c06\u5bcc\u96c6\u7ed3\u679c\u5199\u5165\u6587\u4ef6\uff1a<\/p>\n<p>eG &lt;- enrichGO(gene = g_list,<br \/>\nOrgDb = org.Hs.eg.db,<br \/>\npvalueCutoff = 0.01,<br \/>\nqvalueCutoff = 0.01,<br \/>\nont = &#8220;all&#8221;,<br \/>\nreadable = TRUE)<br \/>\nwrite.table(eG, file = &#8220;eG.txt&#8221;, sep = &#8220;\\t&#8221;, quote = FALSE, row.names = FALSE)<\/p>\n<p>\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u5c0f\u679c\u8bbe\u7f6e\u4e86p\u503c\u548cq\u503c\u7684\u9608\u503c\u4e3a0.01\uff0c\u5e76\u9009\u62e9\u4e86\u6240\u6709\u7684\u529f\u80fd\u5bcc\u96c6\u7c7b\u578b\u3002\u5206\u6790\u7ed3\u675f\u540e\u5c06\u751f\u6210\u4e00\u4e2a\u540d\u4e3a&#8221;eG.txt&#8221;\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542b\u6211\u4eec\u7684\u5bcc\u96c6\u7ed3\u679c\u54e6\u3002\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u5206\u6790\u7684\u7ed3\u679c\u5427\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"342\" class=\"wp-image-24806\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=640%2C342\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?w=2564 2564w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=300%2C161 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=1024%2C548 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=768%2C411 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=1536%2C822 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=2048%2C1096 2048w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?resize=600%2C321 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24804-2.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p><strong>\u591a\u79cd\u65b9\u6cd5\u53ef\u89c6\u5316\u5bcc\u96c6\u5206\u6790\u7ed3\u679c<\/strong><\/p>\n<p>\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u8981\u6559\u5927\u5bb6\u4f7f\u7528enrichplot\u5305\u5bf9\u5bcc\u96c6\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316\uff1a<\/p>\n<ul>\n<li><strong>barplot<\/strong><\/li>\n<\/ul>\n<p>pdf(file = &#8220;eGO_barplot.pdf&#8221;, width = 8, height = 10)<br \/>\nbarplot(eG, x = &#8220;GeneRatio&#8221;, color = &#8220;p.adjust&#8221;,<br \/>\nshowCategory = 10,<br \/>\nsplit = &#8220;ONTOLOGY&#8221;) +<br \/>\nfacet_grid(ONTOLOGY ~ ., scale = &#8216;free&#8217;)<br \/>\ndev.off()<\/p>\n<p>\u6b64\u65f6\u5728\u5de5\u4f5c\u6587\u4ef6\u5939\u4e2d\u5f97\u5230\u4e86pdf\u683c\u5f0f\u7684GO\u5bcc\u96c6\u7ed8\u56fe\uff1a\uff0c\u5176\u4e2d\u5305\u542b\u57fa\u4e8e\u5404\u529f\u80fd\u7c7b\u578b\u7684\u67f1\u72b6\u56fe\u3002\u6bcf\u4e2a\u7c7b\u578b\u4e2d\u663e\u793a\u4e86\u524d10\u4e2a\u5177\u6709\u8c03\u6574\u540ep\u503c\u989c\u8272\u7f16\u7801\u7684\u57fa\u56e0\u6bd4\u4f8b\u3002\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u6548\u679c\u5427\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"800\" class=\"wp-image-24807\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?resize=640%2C800\" alt=\"\u56fe\u8868, \u6761\u5f62\u56fe\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?w=898 898w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?resize=240%2C300 240w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?resize=820%2C1024 820w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?resize=768%2C960 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-7.png?resize=600%2C750 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<ul>\n<li><strong>dotplot<\/strong><\/li>\n<\/ul>\n<p>dotplot(eG, x = &#8220;GeneRatio&#8221;, color = &#8220;p.adjust&#8221;, size = &#8220;Count&#8221;,<br \/>\nshowCategory = 5,<br \/>\nsplit = &#8220;ONTOLOGY&#8221;) +<br \/>\nfacet_grid(ONTOLOGY ~ ., scale = &#8216;free&#8217;)<\/p>\n<p>\u8fd9\u5c06\u751f\u6210\u53e6\u4e00\u4e2a\u6563\u70b9\u56fe\uff0c\u5176\u4e2d\u5305\u542b\u57fa\u4e8e\u5404\u529f\u80fd\u7c7b\u578b\u7684\u70b9\u56fe\u3002\u6bcf\u4e2a\u7c7b\u578b\u4e2d\u663e\u793a\u4e86\u524d5\u4e2a\u57fa\u56e0\u6bd4\u4f8b\uff0c\u5e76\u6839\u636e\u8c03\u6574\u540ep\u503c\u6765\u8bbe\u7f6e\u70b9\u7684\u989c\u8272\u548c\u5927\u5c0f\u3002\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u6548\u679c\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"805\" class=\"wp-image-24808\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-8.png?resize=640%2C805\" alt=\"\u56fe\u8868, \u6563\u70b9\u56fe\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-8.png?w=761 761w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-8.png?resize=239%2C300 239w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/unnamed-file-8.png?resize=600%2C755 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" 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