{"id":26848,"date":"2024-01-29T17:22:32","date_gmt":"2024-01-29T09:22:32","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26848"},"modified":"2024-01-29T17:22:35","modified_gmt":"2024-01-29T09:22:35","slug":"%e6%95%b0%e6%8d%ae%e6%95%b4%e7%90%86%e3%80%81%e6%b3%a8%e9%87%8a%e5%92%8c%e8%a7%a3%e9%87%8a%e4%bd%bc%e4%bd%bc%e8%80%85-annotate-r%e5%8c%85","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26848","title":{"rendered":"\u6570\u636e\u6574\u7406\u3001\u6ce8\u91ca\u548c\u89e3\u91ca\u4f7c\u4f7c\u8005\u00a0\u2014\u00a0annotate\u00a0R\u5305"},"content":{"rendered":"

\u5728\u6570\u636e\u6574\u7406\u3001\u6ce8\u91ca\u548c\u89e3\u91ca\u65b9\u9762\uff0cR\u8bed\u8a00\u5305annotate\u65e0\u7591\u662f\u4e00\u4e2a\u4f7c\u4f7c\u8005\u7684\u5b58\u5728<\/p>\n

R\u8bed\u8a00\u5305annotate\u662f\u4e00\u4e2a\u5e7f\u6cdb\u7528\u4e8e\u751f\u7269\u5b66\u7814\u7a76\u7684\u529f\u80fd\u5f3a\u5927\u7684\u5de5\u5177\u3002\u5b83\u662f\u7531Bioconductor\u9879\u76ee\u5f00\u53d1\u7684\u3002Bioconductor\u662f\u4e00\u4e2a\u9762\u5411\u751f\u7269\u5b66\u548c\u751f\u7269\u533b\u5b66\u9886\u57df\u7684\u5f00\u6e90\u9879\u76ee\uff0c\u4e13\u6ce8\u4e8e\u4e3a\u9ad8\u901a\u91cf\u751f\u7269\u6570\u636e\u5206\u6790\u63d0\u4f9b\u4e30\u5bcc\u7684R\u8bed\u8a00\u5de5\u5177\u548c\u8d44\u6e90\u3002annotate\u5305\u662fBioconductor\u9879\u76ee\u4e2d\u7684\u4e00\u90e8\u5206\uff0c\u4e3b\u8981\u7528\u4e8e\u751f\u7269\u5b66\u6570\u636e\u7684\u6ce8\u91ca\u548c\u529f\u80fd\u89e3\u91ca\u3002<\/p>\n

annotate\u5305\u63d0\u4f9b\u4e86\u5bf9\u57fa\u56e0\u3001\u8f6c\u5f55\u7ec4\u3001\u86cb\u767d\u8d28\u7b49\u751f\u7269\u5b66\u5b9e\u4f53\u8fdb\u884c\u6ce8\u91ca\u7684\u529f\u80fd\uff0c\u5e76\u652f\u6301\u5c06\u5b9e\u4f53\u4e0e\u751f\u7269\u5b66\u6570\u636e\u5e93\u4e2d\u7684\u6ce8\u91ca\u4fe1\u606f\u8fdb\u884c\u5173\u8054\u3002\u901a\u8fc7\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6280\u672f\uff0c\u6211\u4eec\u80fd\u591f\u83b7\u5f97\u5927\u91cf\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u3002\u7136\u800c\uff0c\u8fd9\u4e9b\u6570\u636e\u672c\u8eab\u5e76\u4e0d\u5177\u6709\u76f4\u89c2\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002\u8fd9\u65f6\uff0cannotate\u5305\u53d1\u6325\u4e86\u5b83\u7684\u4f5c\u7528\u3002<\/p>\n

annotate\u5305\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u5c06\u57fa\u56e0ID\u6620\u5c04\u5230\u5bf9\u5e94\u7684\u57fa\u56e0\u7b26\u53f7\u6216\u540d\u79f0\uff0c\u4ece\u800c\u66f4\u65b9\u4fbf\u5730\u5bf9\u57fa\u56e0\u8fdb\u884c\u8bc6\u522b\u548c\u5206\u6790\u3002\u6b64\u5916\uff0cannotate\u8fd8\u80fd\u5c06\u57fa\u56e0\u5206\u7c7b\u4e3a\u4e0d\u540c\u7684\u751f\u7269\u5b66\u7279\u5f81\uff0c\u4f8b\u5982\u8f6c\u5f55\u672c\u7684\u5916\u663e\u5b50\u7ed3\u6784\u3001\u542f\u52a8\u5b50\u533a\u57df\u548c\u8f6c\u5f55\u56e0\u5b50\u7ed3\u5408\u4f4d\u70b9\u7b49\u3002\u8fd9\u4e9b\u4fe1\u606f\u5bf9\u4e8e\u7406\u89e3\u57fa\u56e0\u7684\u529f\u80fd\u548c\u8c03\u63a7\u673a\u5236\u81f3\u5173\u91cd\u8981\u3002<\/p>\n

\u8981\u4f7f\u7528annotate\u5305\uff0c\u53ef\u4ee5\u5728R\u4e2d\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\u8fdb\u884c\u5b89\u88c5\u548c\u52a0\u8f7d\uff1a<\/p>\n

> install.packages(“annotate”) #\u5b89\u88c5annotate\u8bed\u8a00\u5305<\/p>\n

> library(annotate) #\u52a0\u8f7d\u8bed\u8a00\u5305<\/p>\n

annotate\u5305\u4e3a\u7528\u6237\u63d0\u4f9b\u4e86\u5904\u7406\u57fa\u56e0\u3001\u8f6c\u5f55\u7ec4\u3001\u86cb\u767d\u8d28\u7b49\u751f\u7269\u5b66\u5b9e\u4f53\u7684\u529f\u80fd\uff0c\u5176\u4e2d\u5305\u62ec\u5c06\u5b83\u4eec\u4e0e\u751f\u7269\u5b66\u6570\u636e\u5e93\u4e2d\u7684\u6ce8\u91ca\u4fe1\u606f\u8fdb\u884c\u5173\u8054\u3002\u8fd9\u4e9b\u6ce8\u91ca\u4fe1\u606f\u53ef\u80fd\u5305\u62ec\u57fa\u56e0\u7684\u7b26\u53f7\u3001\u63cf\u8ff0\u3001\u901a\u8def\u5173\u8054\u3001\u7ec6\u80de\u7ec4\u5206\u7b49\uff0c\u8fd9\u5bf9\u4e8e\u751f\u7269\u5b66\u7814\u7a76\u975e\u5e38\u6709\u4ef7\u503c\u3002\u901a\u8fc7annotate\u5305\uff0c\u7814\u7a76\u4eba\u5458\u80fd\u591f\u8f7b\u677e\u5730\u5bf9\u751f\u7269\u5b66\u6570\u636e\u8fdb\u884c\u6574\u7406\u3001\u6ce8\u91ca\u548c\u89e3\u91ca\uff0c\u4ece\u800c\u4e3a\u8fdb\u4e00\u6b65\u7684\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76\u548c\u751f\u7269\u5b66\u63a2\u7d22\u63d0\u4f9b\u4e86\u5f3a\u5927\u7684\u5de5\u5177\u3002<\/p>\n

\u5728\u8f6c\u5f55\u7ec4\u6570\u636e\u5206\u6790\u4e2d\uff0cannotate\u5305\u4e5f\u80fd\u5c06\u57fa\u56e0\u4e0e\u7279\u5b9a\u7684\u751f\u7269\u8fc7\u7a0b\u3001\u7ec6\u80de\u7ec4\u5206\u4ee5\u53ca\u901a\u8def\u76f8\u5173\u8054\u3002\u8fd9\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u5b9d\u8d35\u7684\u7ebf\u7d22\uff0c\u5e2e\u52a9\u4ed6\u4eec\u89e3\u91ca\u57fa\u56e0\u8868\u8fbe\u7684\u751f\u7269\u5b66\u610f\u4e49\u3002\u901a\u8fc7annotate\u5305\u7684\u529f\u80fd\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u66f4\u597d\u5730\u7406\u89e3\u4e0d\u540c\u6761\u4ef6\u4e0b\u57fa\u56e0\u7684\u8868\u8fbe\u6a21\u5f0f\uff0c\u53d1\u73b0\u5173\u952e\u7684\u751f\u7269\u5b66\u901a\u8def\u548c\u673a\u5236\u3002<\/p>\n

\u793a\u4f8b\uff1a<\/p>\n

\u5728R\u4e2d\u4f7f\u7528annotate\u5305\u6765\u5c06\u57fa\u56e0\u4e0e\u7279\u5b9a\u7684\u751f\u7269\u8fc7\u7a0b\u3001\u7ec6\u80de\u7ec4\u5206\u4ee5\u53ca\u901a\u8def\u76f8\u5173\u8054\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\uff08Gene Set Enrichment Analysis, GSEA\uff09\u4f5c\u4e3a\u793a\u4f8b\u3002GSEA\u662f\u4e00\u79cd\u5e38\u7528\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u65b9\u6cd5\uff0c\u5b83\u7528\u4e8e\u8bc6\u522b\u5728\u7ed9\u5b9a\u8f6c\u5f55\u7ec4\u6570\u636e\u4e2d\u4e0e\u7279\u5b9a\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u7ec6\u80de\u7ec4\u5206\u6216\u901a\u8def\u76f8\u5173\u8054\u7684\u57fa\u56e0\u96c6\u5408\u3002<\/p>\n

# \u5b89\u88c5\u548c\u52a0\u8f7d\u5fc5\u8981\u7684\u5305<\/p>\n

> install.packages(“annotate”)<\/p>\n

> library(annotate)<\/p>\n

> library(clusterProfiler)<\/p>\n

# \u793a\u4f8b\u6570\u636e\u96c6<\/p>\n

> set.seed(42)<\/p>\n

> gene_names <- paste(“Gene”, 1:100, sep=””)<\/p>\n

> expression_data <- matrix(rnorm(1000, mean = 10, sd = 2), nrow = 100, ncol = 10, dimnames = list(gene_names, c(“Sample1”, “Sample2”, “Sample3”, “Sample4”, “Sample5”, “Sample6”, “Sample7”, “Sample8”, “Sample9”, “Sample10”)))<\/p>\n

> gene_annotation <- data.frame(<\/p>\n

+ GeneID = gene_names,<\/p>\n

+ Pathway = sample(c(“Pathway_A”, “Pathway_B”, “Pathway_C”), size = 100, replace = TRUE),<\/p>\n

+ CellularComponent = sample(c(“Component_X”, “Component_Y”, “Component_Z”), size = 100, replace = TRUE)<\/p>\n

+ )<\/p>\n

# \u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790<\/p>\n

> enrichment_results <- gene_set_enrichment(annotation = gene_annotation, gene_expression = expression_data, by = “Pathway”)<\/p>\n

# \u67e5\u770b\u5bcc\u96c6\u5206\u6790\u7ed3\u679c<\/p>\n

> print(enrichment_results)<\/p>\n

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

\"Screenshot<\/p>\n

\u9664\u4e86\u8f6c\u5f55\u7ec4\u6570\u636e\uff0cannotate\u5305\u8fd8\u53ef\u4ee5\u5904\u7406\u5176\u4ed6\u7c7b\u578b\u7684\u751f\u7269\u5b66\u6570\u636e\u3002\u4f8b\u5982\uff0c\u5b83\u53ef\u4ee5\u7528\u4e8e\u5904\u7406\u86cb\u767d\u8d28\u4e92\u4f5c\u7f51\u7edc\u6570\u636e\uff0c\u5c06\u86cb\u767d\u8d28ID\u6ce8\u91ca\u4e3a\u86cb\u767d\u8d28\u540d\u79f0\u548c\u529f\u80fd\u6ce8\u91ca\u3002\u8fd9\u5bf9\u4e8e\u7814\u7a76\u86cb\u767d\u8d28\u95f4\u7684\u76f8\u4e92\u4f5c\u7528\u548c\u4fe1\u53f7\u4f20\u5bfc\u9014\u5f84\u975e\u5e38\u6709\u5e2e\u52a9\u3002<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305annotate\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0c\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\uff0c\u7406\u89e3\u548c\u89e3\u91ca\u6570\u636e\u662f\u81f3\u5173\u91cd\u8981\u7684\u3002annotate\u5305\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u5e2e\u52a9\u4ed6\u4eec\u5bf9\u57fa\u56e0\u548c\u86cb\u767d\u8d28\u6570\u636e\u8fdb\u884c\u529f\u80fd\u6ce8\u91ca\u548c\u89e3\u91ca\u3002\u901a\u8fc7annotate\u5305\uff0c\u7814\u7a76\u4eba\u5458\u80fd\u591f\u66f4\u6df1\u5165\u5730\u6316\u6398\u6570\u636e\u80cc\u540e\u7684\u751f\u7269\u5b66\u610f\u4e49\uff0c\u4ece\u800c\u4e3a\u751f\u547d\u79d1\u5b66\u9886\u57df\u7684\u8fdb\u4e00\u6b65\u7814\u7a76\u63d0\u4f9b\u6709\u529b\u652f\u6301\u3002<\/p>\n

\u5c0f\u4f19\u4f34\u4eec\uff0c\u4eca\u5929\u6709\u6ca1\u6709\u5b66\u5230\u65b0\u77e5\u8bc6\u5462\uff0c\u60f3\u8981\u7ee7\u7eed\u4e86\u89e3R\u8bed\u8a00\u5185\u5bb9\u53ef\u4ee5\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff5e\uff5e\u6216\u8005\u4e5f\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u5b98\u7f51\u4e5f\u4f1a\u6301\u7eed\u66f4\u65b0\u7684\u54e6\uff5e http:\/\/www.biocloudservice.com\/home.html<\/a><\/p>\n

References:<\/p>\n

    \n
  1. https:\/\/learn.gencore.bio.nyu.edu\/rna-seq-analysis\/gene-set-enrichment-analysis\/<\/a><\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

    \u5728\u6570\u636e\u6574\u7406\u3001\u6ce8\u91ca\u548c\u89e3\u91ca\u65b9\u9762\uff0cR\u8bed\u8a00\u5305annotate\u65e0\u7591\u662f\u4e00\u4e2a\u4f7c\u4f7c\u8005\u7684\u5b58\u5728 R\u8bed\u8a00\u5305annotate\u662f\u4e00\u4e2a\u5e7f\u6cdb […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26848"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=26848"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26848\/revisions"}],"predecessor-version":[{"id":26855,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26848\/revisions\/26855"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26848"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26848"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26848"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}