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style=\"text-indent: 0em;white-space: normal;\"><br \/><\/p>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\">\u4ee3\u7801\u4e2d\u5bf9\u9009\u5b9a\u7684\u57fa\u56e0brca1\u8868\u8fbe\u91cf\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\u3002\u4e0b\u9762\u662f\u4e0b\u8f7d\u7684GO\u548cKEGGgmt\u6587\u4ef6\uff0c\u65b9\u4fbf\u540e\u7eed\u4f7f\u7528R\u5305”org.Hs.eg.db”\u3001”DOSE”\u3001”clusterProfiler”\u548c”enrichplot”\u5206\u6790\u3002<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 50%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3010989010989011\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_zckX2wEMvicwy6w0MtkHArLQ8qR1aw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82qickVhzm9p2E6K3ib3hciasibpEpyzckX2wEMvicwy6w0MtkHArLQ8qR1aw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"455\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 50%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.255656108597285\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_MrxvlianGeqSEXUz5cgIWicp5WuHOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82WIgADOQBXvL1ttPgEcOFamo6V4MrxvlianGeqSEXUz5cgIWicp5WuHOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"442\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"colorspace\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"stringi\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"ggplot2\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u5b89\u88c5\u4e09\u4e2aR\u5305\uff1a<span class=\"code-snippet__string\">\"colorspace\"<\/span>\u3001<span class=\"code-snippet__string\">\"stringi\"<\/span>\u548c<span class=\"code-snippet__string\">\"ggplot2\"<\/span>\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">\u8fd9\u4e9b\u5305\u53ef\u80fd\u662f\u540e\u7eed\u4ee3\u7801\u8fd0\u884c\u6240\u9700\u7684\u4f9d\u8d56\u5305\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># install.packages(\"BiocManager\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"limma\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"org.Hs.eg.db\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"DOSE\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"clusterProfiler\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"enrichplot\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u751f\u7269\u4fe1\u606f\u5b66\u548c\u5bcc\u96c6\u5206\u6790\u76f8\u5173\u7684R\u5305\uff0c\u8fd9\u4e9b\u5305\u5305\u62ec\uff1a<span class=\"code-snippet__string\">\"BiocManager\"<\/span>\u3001<span class=\"code-snippet__string\">\"limma\"<\/span>\u3001<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>\u3001<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"DOSE\"<\/span>\u3001<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>\u548c<span class=\"code-snippet__string\">\"enrichplot\"<\/span>\u3002\u8fd9\u4e9b\u5305\u63d0\u4f9b\u4e86\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u6240\u9700\u7684\u51fd\u6570\u548c\u6570\u636e\u5e93\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Hs.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><code><span class=\"code-snippet_outer\">library(enrichplot)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"library\"<\/span>\u51fd\u6570\u52a0\u8f7d\u4e86\u4e4b\u524d\u5b89\u88c5\u7684\u56db\u4e2a\u5305\uff1a<span class=\"code-snippet__string\">\"limma\"<\/span>\u3001<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>\u3001<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>\u548c<span class=\"code-snippet__string\">\"enrichplot\"<\/span>\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u4f7f\u5f97\u8fd9\u4e9b\u5305\u7684\u51fd\u6570\u53ef\u4ee5\u5728\u540e\u7eed\u4ee3\u7801\u4e2d\u4f7f\u7528\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">\u5b9a\u4e49\u4e86\u53d8\u91cf<span class=\"code-snippet__string\">\"gene\"<\/span>\uff0c\u8868\u793a\u611f\u5174\u8da3\u7684\u57fa\u56e0\u540d\u79f0\uff0c\u4ee5\u53ca\u53d8\u91cf<span class=\"code-snippet__string\">\"gmtFile\"<\/span>\uff0c\u8868\u793a\u57fa\u56e0\u96c6\u6587\u4ef6\u7684\u540d\u79f0\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">gene=<span class=\"code-snippet__string\">\"BRCA1\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gmtFile=<span class=\"code-snippet__string\">\"c5.all.v7.1.symbols.gmt\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u56e0\u96c6\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\"read.gmt\"\u51fd\u6570\u4ece\u6307\u5b9a\u7684\u57fa\u56e0\u96c6\u6587\u4ef6\"gmtFile\"\u4e2d\u8bfb\u53d6\u57fa\u56e0\u96c6\u4fe1\u606f\uff0c\u5c06\u57fa\u56e0\u96c6\u5b58\u50a8\u5728\u53d8\u91cf\"gmt\"\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gmt=read.gmt(gmtFile)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u83b7\u53d6\u76ee\u5f55\u4e0b\u7684\u6240\u6709\u80bf\u7624\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">files=dir()<\/span><\/code><code><span class=\"code-snippet_outer\">files=grep(<span class=\"code-snippet__string\">\"^symbol.\"<\/span>,files,value=<span class=\"code-snippet__built_in\">T<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">\u83b7\u53d6\u5f53\u524d\u5de5\u4f5c\u76ee\u5f55\u4e0b\u6240\u6709\u4ee5<span class=\"code-snippet__string\">\"symbol.\"<\/span>\u5f00\u5934\u7684\u6587\u4ef6\u540d\uff0c\u5c06\u8fd9\u4e9b\u6587\u4ef6\u540d\u5b58\u50a8\u5728\u53d8\u91cf<span class=\"code-snippet__string\">\"files\"<\/span>\u4e2d\u3002\u8fd9\u91cc\u7684\u6587\u4ef6\u540d\u53ef\u80fd\u662f\u80bf\u7624\u7684\u6570\u636e\u6587\u4ef6\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u4ee5<span class=\"code-snippet__string\">\"symbol.\"<\/span>\u5f00\u5934\u53ef\u80fd\u662f\u56e0\u4e3a\u8fd9\u4e9b\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4f7f\u7528\u57fa\u56e0\u7b26\u53f7\uff08symbol\uff09\u4f5c\u4e3a\u5217\u540d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(i <span class=\"code-snippet__keyword\">in<\/span> files){<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u5f53\u524d\u80bf\u7624\u6570\u636e\u6587\u4ef6\uff0c\u5c06\u6570\u636e\u5b58\u50a8\u5728\u53d8\u91cf\"rt\"\u4e2d\u3002\u63d0\u53d6\u80bf\u7624\u7c7b\u578b\u540d\u79f0\uff0c\u7528\u4e8e\u540e\u7eed\u8f93\u51fa\u6587\u4ef6\u7684\u547d\u540d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(i,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">CancerType=gsub(<span class=\"code-snippet__string\">\"^symbol\\.|\\.txt$\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,i)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406\uff1a\u5982\u679c\u4e00\u4e2a\u57fa\u56e0\u5360\u4e86\u591a\u884c\uff0c\u53d6\u5176\u5747\u503c\u4f5c\u4e3a\u8be5\u57fa\u56e0\u7684\u8868\u8fbe\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(rt)<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(rt)=rt[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">exp<\/span>=rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">list<\/span>(rownames(<span class=\"code-snippet__built_in\">exp<\/span>),colnames(<span class=\"code-snippet__built_in\">exp<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=matrix(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.matrix(<span class=\"code-snippet__built_in\">exp<\/span>)),nrow=nrow(<span class=\"code-snippet__built_in\">exp<\/span>),<span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">dimnames<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(data)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u9664\u6b63\u5e38\u6837\u54c1\uff1a\u6839\u636e\u6837\u672c\u7684\u547d\u540d\u89c4\u5219\uff08\u5176\u4e2d\"-\"\u5206\u9694\uff09\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7b5b\u9009\u51fa\u6b63\u5e38\u6837\u54c1\uff08\u547d\u540d\u4e2d\u4e0d\u5305\u542b\"2\"\uff09\uff0c\u5e76\u5c06\u8fd9\u4e9b\u6837\u54c1\u4ece\u6570\u636e\u4e2d\u5220\u9664\u3002\u56e0\u4e3a\u8fd9\u91cc\u7684\u5bcc\u96c6\u5206\u6790\u4e3b\u8981\u5173\u6ce8\u764c\u75c7\u6837\u672c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(colnames(data),<span class=\"code-snippet__string\">\"\\-\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(group,<span class=\"code-snippet__string\">\"\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=gsub(<span class=\"code-snippet__string\">\"2\"<\/span>,<span class=\"code-snippet__string\">\"1\"<\/span>,group)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[,group==<span class=\"code-snippet__number\">0<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6309\u76ee\u6807\u57fa\u56e0\u5c06\u6837\u54c1\u5206\u6210\u9ad8\u4f4e\u8868\u8fbe\u4e24\u7ec4,\u6839\u636e\u6307\u5b9a\u7684\u57fa\u56e0\uff08gene\uff09\u5c06\u6837\u672c\u5206\u6210\u9ad8\u8868\u8fbe\u7ec4\u548c\u4f4e\u8868\u8fbe\u7ec4\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u57fa\u4e8e\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u7684\u4e2d\u4f4d\u6570\u6765\u5206\u7ec4\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dataL=data[,(data[gene,]<=median(data[gene,]))]<\/span><\/code><code><span class=\"code-snippet_outer\">dataH=data[,(data[gene,]>median(data[gene,]))]<\/span><\/code><code><span class=\"code-snippet_outer\">meanL=rowMeans(dataL)<\/span><\/code><code><span class=\"code-snippet_outer\">meanH=rowMeans(dataH)<\/span><\/code><code><span class=\"code-snippet_outer\">meanL[meanL<<span class=\"code-snippet__number\">0.00001<\/span>]=<span class=\"code-snippet__number\">0.00001<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">meanH[meanH<<span class=\"code-snippet__number\">0.00001<\/span>]=<span class=\"code-snippet__number\">0.00001<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFC=log2(meanH\/meanL)<\/span><\/code><code><span class=\"code-snippet_outer\">logFC=sort(logFC,decreasing=<span class=\"code-snippet__built_in\">T<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u57fa\u56e0\u7684logFC\uff08log2 fold change\uff09\u503c\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7528\u6765\u8861\u91cf\u5728\u9ad8\u8868\u8fbe\u7ec4\u4e0e\u4f4e\u8868\u8fbe\u7ec4\u4e4b\u95f4\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790GSEA\uff08Gene Set Enrichment Analysis\uff09\u6765\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u901a\u8fc7\u8c03\u7528GSEA\u51fd\u6570GSEA(logFC, TERM2GENE=gmt, nPerm=100, pvalueCutoff=1)\u6765\u6267\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5176\u4e2dlogFC\u662f\u57fa\u56e0\u7684logFC\u503c\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#TERM2GENE\u662f\u57fa\u56e0\u96c6\u6570\u636e\u5e93\uff0cnPerm\u662f\u968f\u673a\u91cd\u6392\u7684\u6b21\u6570\uff0cpvalueCutoff\u662f\u8bbe\u5b9a\u7684p\u503c\u9608\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">kk=GSEA(logFC,TERM2GENE=gmt, nPerm=<span class=\"code-snippet__number\">100<\/span>,pvalueCutoff = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">kkTab=as.data.frame(kk)<\/span><\/code><code><span class=\"code-snippet_outer\">kkTab=kkTab[kkTab$pvalue<<span class=\"code-snippet__number\">0.05<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(kkTab,file=paste0(<span class=\"code-snippet__string\">\"Term.\"<\/span>,CancerType,<span class=\"code-snippet__string\">\".txt\"<\/span>),sep=<span class=\"code-snippet__string\">\"t\"<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>,row.names = <span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4fdd\u5b58\u4e3a\u4e00\u4e2a\u6570\u636e\u6846kkTab\uff0c\u5e76\u5c06p\u503c\u5c0f\u4e8e0.05\u7684\u5bcc\u96c6\u7ed3\u679c\u7b5b\u9009\u51fa\u6765\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u5199\u5165\u540d\u4e3a\"Term..txt\"\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5176\u4e2dCancerType\u662f\u80bf\u7624\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u5bcc\u96c6\u7684\u56fe\u5f62<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6709\u81f3\u5c115\u4e2a\u5bcc\u96c6\u9879\uff0c\u5219\u8f93\u51fa\u524d5\u4e2a\u5bcc\u96c6\u56fe\u5f62\uff0c\u6bcf\u4e2a\u56fe\u5f62\u4fdd\u5b58\u4e3a\u4e00\u4e2aPDF\u6587\u4ef6\uff0c\u6587\u4ef6\u540d\u4e3a\"Term..pdf\"\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5176\u4e2dCancerType\u662f\u80bf\u7624\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">termNum=<span class=\"code-snippet__number\">5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span>(nrow(kkTab)>=termNum){<\/span><\/code><code><span class=\"code-snippet_outer\">gseaplot=gseaplot2(kk, row.names(kkTab)[<span class=\"code-snippet__number\">1<\/span>:termNum],base_size =<span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=paste0(<span class=\"code-snippet__string\">\"Term.\"<\/span>,CancerType,<span class=\"code-snippet__string\">\".pdf\"<\/span>),width=<span class=\"code-snippet__number\">8<\/span>,height=<span class=\"code-snippet__number\">6<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">print(gseaplot)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 45.9582%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"3.4020100502512562\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_F0r3QS1a74VySic9z0Bx0SzduTI7gA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82dVzQ3xwt0dicJbqlObkzLVcPbUF0r3QS1a74VySic9z0Bx0SzduTI7gA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"199\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.55\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_wlFulrLlrr7YM7onynhLSiaic9XibQ.png?w=640\" 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normal;\">\u4ee5\u4e0a\u5c31\u662f\u5bf9\u7ed9\u5b9a\u7684\u80bf\u7624\u6570\u636e\uff0c\u4ee5\u53ca\u6307\u5b9a\u7684\u57fa\u56e0\u96c6\u6570\u636e\u5e93\uff08gmt\u6587\u4ef6\uff09\uff0c\u8fdb\u884c\u4e86\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\uff0c\u901a\u8fc7\u8f93\u51fa\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u7684\u6587\u672c\u6587\u4ef6\u548c\u5bcc\u96c6\u56fe\u5f62\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4e86\u89e3\u5728\u4e0d\u540c\u80bf\u7624\u7c7b\u578b\u4e2d\u4e0e<span style=\"text-indent: 0em;\">\u6307\u5b9a\u57fa\u56e0\u76f8\u5173\u7684\u751f\u7269\u5b66\u529f\u80fd\u548c\u901a\u8def\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><span style=\"text-indent: 0em;\"><br \/><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: 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style=\"font-size: 6px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;border-width: 1px;border-style: solid;border-color: rgba(255, 255, 255, 0);background-color: rgb(232, 250, 150);text-align: center;width: 1.8em;height: 1.8em;line-height: 1.8em;border-radius: 100%;margin-left: auto;margin-right: auto;color: transparent;\">\n<p>1<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"margin-bottom: 24px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_BoDuficWb7YjnP0CXo0mIcibhsXn8w-1.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEUlxqHhbZryhECGXicgBrLn1ZkgkpYia2qsgSgNWPQMp0RiaIAmlBoDuficWb7YjnP0CXo0mIcibhsXn8w\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"margin-bottom: 24px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5555555555555556\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_akXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ-5.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEXjjmsEC5aXz0RE4be2ib1fJPnBD8yX0Z6OF2zocd2ngHpLOakXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"display: none;margin-bottom: 24px;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br 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[…]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/59453"}],"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=59453"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59453\/revisions"}],"predecessor-version":[{"id":59462,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/59453\/revisions\/59462"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=59453"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=59453"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=59453"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

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normal;\">\u6211\u4eec\u5bf9\u7ed9\u5b9a\u7684\u80bf\u7624\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\uff0c\u4ee5\u5bfb\u627e\u4e0e\u6307\u5b9a\u57fa\u56e0\uff08\u4f8b\u5982BRCA1\uff09\u76f8\u5173\u7684\u751f\u7269\u5b66\u529f\u80fd\u548c\u901a\u8def\u3002\u8fd9\u5bf9\u4e8e\u6df1\u5165\u7406\u89e3\u57fa\u56e0\u5728\u4e0d\u540c\u80bf\u7624\u7c7b\u578b\u4e2d\u7684\u529f\u80fd\u4ee5\u53ca\u4e0e\u80bf\u7624\u53d1\u751f\u548c\u53d1\u5c55\u76f8\u5173\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u975e\u5e38\u91cd\u8981\u3002\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u662f\u4e00\u79cd\u5e38\u7528\u7684\u751f\u7269\u4fe1\u606f\u5b66\u65b9\u6cd5\uff0c\u5b83\u53ef\u4ee5\u901a\u8fc7\u6bd4\u8f83\u57fa\u56e0\u96c6\u5185\u7684\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u7684\u8868\u8fbe\u6a21\u5f0f\uff0c\u627e\u51fa\u4e0e\u8be5\u57fa\u56e0\u96c6\u76f8\u5173\u8054\u7684\u751f\u7269\u5b66\u8fc7\u7a0b\u3001\u901a\u8def\u6216\u529f\u80fd\u3002\u8fd9\u79cd\u5206\u6790\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u5728\u9ad8\u901a\u91cf\u6570\u636e\u4e2d\u5bfb\u627e\u751f\u7269\u5b66\u610f\u4e49\u7684\u6709\u529b\u5de5\u5177\uff0c\u6709\u52a9\u4e8e\u8bc6\u522b\u6f5c\u5728\u7684\u9776\u70b9\u3001\u751f\u7269\u6807\u5fd7\u7269\u4ee5\u53ca\u5f00\u5c55\u66f4\u6df1\u5165\u7684\u673a\u5236\u7814\u7a76\u3002<\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><br \/><\/p>\n<\/section>\n<p style=\"white-space: normal;\" powered-by=\"xiumi.us\">\u4ee3\u7801\u4e2d\u5bf9\u9009\u5b9a\u7684\u57fa\u56e0brca1\u8868\u8fbe\u91cf\u8fdb\u884c\u5bcc\u96c6\u5206\u6790\u3002\u4e0b\u9762\u662f\u4e0b\u8f7d\u7684GO\u548cKEGGgmt\u6587\u4ef6\uff0c\u65b9\u4fbf\u540e\u7eed\u4f7f\u7528R\u5305”org.Hs.eg.db”\u3001”DOSE”\u3001”clusterProfiler”\u548c”enrichplot”\u5206\u6790\u3002<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 50%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.3010989010989011\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_zckX2wEMvicwy6w0MtkHArLQ8qR1aw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82qickVhzm9p2E6K3ib3hciasibpEpyzckX2wEMvicwy6w0MtkHArLQ8qR1aw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"455\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 50%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.255656108597285\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_MrxvlianGeqSEXUz5cgIWicp5WuHOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82WIgADOQBXvL1ttPgEcOFamo6V4MrxvlianGeqSEXUz5cgIWicp5WuHOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"442\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"colorspace\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"stringi\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#install.packages(\"ggplot2\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u5b89\u88c5\u4e09\u4e2aR\u5305\uff1a<span class=\"code-snippet__string\">\"colorspace\"<\/span>\u3001<span class=\"code-snippet__string\">\"stringi\"<\/span>\u548c<span class=\"code-snippet__string\">\"ggplot2\"<\/span>\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">\u8fd9\u4e9b\u5305\u53ef\u80fd\u662f\u540e\u7eed\u4ee3\u7801\u8fd0\u884c\u6240\u9700\u7684\u4f9d\u8d56\u5305\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#if (!requireNamespace(\"BiocManager\", quietly = TRUE))<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># install.packages(\"BiocManager\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"limma\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"org.Hs.eg.db\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"DOSE\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"clusterProfiler\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"enrichplot\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">\u751f\u7269\u4fe1\u606f\u5b66\u548c\u5bcc\u96c6\u5206\u6790\u76f8\u5173\u7684R\u5305\uff0c\u8fd9\u4e9b\u5305\u5305\u62ec\uff1a<span class=\"code-snippet__string\">\"BiocManager\"<\/span>\u3001<span class=\"code-snippet__string\">\"limma\"<\/span>\u3001<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>\u3001<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"DOSE\"<\/span>\u3001<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>\u548c<span class=\"code-snippet__string\">\"enrichplot\"<\/span>\u3002\u8fd9\u4e9b\u5305\u63d0\u4f9b\u4e86\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u6240\u9700\u7684\u51fd\u6570\u548c\u6570\u636e\u5e93\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">library(limma)<\/span><\/code><code><span class=\"code-snippet_outer\">library(org.Hs.eg.db)<\/span><\/code><code><span class=\"code-snippet_outer\">library(clusterProfiler)<\/span><\/code><code><span class=\"code-snippet_outer\">library(enrichplot)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__string\">\"library\"<\/span>\u51fd\u6570\u52a0\u8f7d\u4e86\u4e4b\u524d\u5b89\u88c5\u7684\u56db\u4e2a\u5305\uff1a<span class=\"code-snippet__string\">\"limma\"<\/span>\u3001<span class=\"code-snippet__string\">\"org.Hs.eg.db\"<\/span>\u3001<span class=\"code-snippet__string\">\"clusterProfiler\"<\/span>\u548c<span class=\"code-snippet__string\">\"enrichplot\"<\/span>\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u4f7f\u5f97\u8fd9\u4e9b\u5305\u7684\u51fd\u6570\u53ef\u4ee5\u5728\u540e\u7eed\u4ee3\u7801\u4e2d\u4f7f\u7528\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">\u5b9a\u4e49\u4e86\u53d8\u91cf<span class=\"code-snippet__string\">\"gene\"<\/span>\uff0c\u8868\u793a\u611f\u5174\u8da3\u7684\u57fa\u56e0\u540d\u79f0\uff0c\u4ee5\u53ca\u53d8\u91cf<span class=\"code-snippet__string\">\"gmtFile\"<\/span>\uff0c\u8868\u793a\u57fa\u56e0\u96c6\u6587\u4ef6\u7684\u540d\u79f0\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">gene=<span class=\"code-snippet__string\">\"BRCA1\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u56e0\u540d\u79f0<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gmtFile=<span class=\"code-snippet__string\">\"c5.all.v7.1.symbols.gmt\"<\/span> <span class=\"code-snippet__comment\">#\u57fa\u56e0\u96c6\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\"read.gmt\"\u51fd\u6570\u4ece\u6307\u5b9a\u7684\u57fa\u56e0\u96c6\u6587\u4ef6\"gmtFile\"\u4e2d\u8bfb\u53d6\u57fa\u56e0\u96c6\u4fe1\u606f\uff0c\u5c06\u57fa\u56e0\u96c6\u5b58\u50a8\u5728\u53d8\u91cf\"gmt\"\u4e2d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gmt=read.gmt(gmtFile)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u83b7\u53d6\u76ee\u5f55\u4e0b\u7684\u6240\u6709\u80bf\u7624\u6570\u636e\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">files=dir()<\/span><\/code><code><span class=\"code-snippet_outer\">files=grep(<span class=\"code-snippet__string\">\"^symbol.\"<\/span>,files,value=<span class=\"code-snippet__built_in\">T<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">\u83b7\u53d6\u5f53\u524d\u5de5\u4f5c\u76ee\u5f55\u4e0b\u6240\u6709\u4ee5<span class=\"code-snippet__string\">\"symbol.\"<\/span>\u5f00\u5934\u7684\u6587\u4ef6\u540d\uff0c\u5c06\u8fd9\u4e9b\u6587\u4ef6\u540d\u5b58\u50a8\u5728\u53d8\u91cf<span class=\"code-snippet__string\">\"files\"<\/span>\u4e2d\u3002\u8fd9\u91cc\u7684\u6587\u4ef6\u540d\u53ef\u80fd\u662f\u80bf\u7624\u7684\u6570\u636e\u6587\u4ef6\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\">\u4ee5<span class=\"code-snippet__string\">\"symbol.\"<\/span>\u5f00\u5934\u53ef\u80fd\u662f\u56e0\u4e3a\u8fd9\u4e9b\u6587\u4ef6\u4e2d\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4f7f\u7528\u57fa\u56e0\u7b26\u53f7\uff08symbol\uff09\u4f5c\u4e3a\u5217\u540d\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span>(i <span class=\"code-snippet__keyword\">in<\/span> files){<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8bfb\u53d6\u5f53\u524d\u80bf\u7624\u6570\u636e\u6587\u4ef6\uff0c\u5c06\u6570\u636e\u5b58\u50a8\u5728\u53d8\u91cf\"rt\"\u4e2d\u3002\u63d0\u53d6\u80bf\u7624\u7c7b\u578b\u540d\u79f0\uff0c\u7528\u4e8e\u540e\u7eed\u8f93\u51fa\u6587\u4ef6\u7684\u547d\u540d\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=read.table(i,sep=<span class=\"code-snippet__string\">\"t\"<\/span>,header=<span class=\"code-snippet__built_in\">T<\/span>,check.names=<span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">CancerType=gsub(<span class=\"code-snippet__string\">\"^symbol\\.|\\.txt$\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,i)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bf9\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u8fdb\u884c\u9884\u5904\u7406\uff1a\u5982\u679c\u4e00\u4e2a\u57fa\u56e0\u5360\u4e86\u591a\u884c\uff0c\u53d6\u5176\u5747\u503c\u4f5c\u4e3a\u8be5\u57fa\u56e0\u7684\u8868\u8fbe\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">rt=as.matrix(rt)<\/span><\/code><code><span class=\"code-snippet_outer\">rownames(rt)=rt[,<span class=\"code-snippet__number\">1<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">exp<\/span>=rt[,<span class=\"code-snippet__number\">2<\/span>:ncol(rt)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">list<\/span>(rownames(<span class=\"code-snippet__built_in\">exp<\/span>),colnames(<span class=\"code-snippet__built_in\">exp<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">data=matrix(<span class=\"code-snippet__built_in\">as.numeric<\/span>(as.matrix(<span class=\"code-snippet__built_in\">exp<\/span>)),nrow=nrow(<span class=\"code-snippet__built_in\">exp<\/span>),<span class=\"code-snippet__built_in\">dimnames<\/span>=<span class=\"code-snippet__built_in\">dimnames<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">data=avereps(data)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5220\u9664\u6b63\u5e38\u6837\u54c1\uff1a\u6839\u636e\u6837\u672c\u7684\u547d\u540d\u89c4\u5219\uff08\u5176\u4e2d\"-\"\u5206\u9694\uff09\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7b5b\u9009\u51fa\u6b63\u5e38\u6837\u54c1\uff08\u547d\u540d\u4e2d\u4e0d\u5305\u542b\"2\"\uff09\uff0c\u5e76\u5c06\u8fd9\u4e9b\u6837\u54c1\u4ece\u6570\u636e\u4e2d\u5220\u9664\u3002\u56e0\u4e3a\u8fd9\u91cc\u7684\u5bcc\u96c6\u5206\u6790\u4e3b\u8981\u5173\u6ce8\u764c\u75c7\u6837\u672c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(colnames(data),<span class=\"code-snippet__string\">\"\\-\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">4<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=sapply(strsplit(group,<span class=\"code-snippet__string\">\"\"<\/span>),<span class=\"code-snippet__string\">\"[\"<\/span>,<span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">group=gsub(<span class=\"code-snippet__string\">\"2\"<\/span>,<span class=\"code-snippet__string\">\"1\"<\/span>,group)<\/span><\/code><code><span class=\"code-snippet_outer\">data=data[,group==<span class=\"code-snippet__number\">0<\/span>]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6309\u76ee\u6807\u57fa\u56e0\u5c06\u6837\u54c1\u5206\u6210\u9ad8\u4f4e\u8868\u8fbe\u4e24\u7ec4,\u6839\u636e\u6307\u5b9a\u7684\u57fa\u56e0\uff08gene\uff09\u5c06\u6837\u672c\u5206\u6210\u9ad8\u8868\u8fbe\u7ec4\u548c\u4f4e\u8868\u8fbe\u7ec4\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u57fa\u4e8e\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u7684\u4e2d\u4f4d\u6570\u6765\u5206\u7ec4\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dataL=data[,(data[gene,]<=median(data[gene,]))]<\/span><\/code><code><span class=\"code-snippet_outer\">dataH=data[,(data[gene,]>median(data[gene,]))]<\/span><\/code><code><span class=\"code-snippet_outer\">meanL=rowMeans(dataL)<\/span><\/code><code><span class=\"code-snippet_outer\">meanH=rowMeans(dataH)<\/span><\/code><code><span class=\"code-snippet_outer\">meanL[meanL<<span class=\"code-snippet__number\">0.00001<\/span>]=<span class=\"code-snippet__number\">0.00001<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">meanH[meanH<<span class=\"code-snippet__number\">0.00001<\/span>]=<span class=\"code-snippet__number\">0.00001<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">logFC=log2(meanH\/meanL)<\/span><\/code><code><span class=\"code-snippet_outer\">logFC=sort(logFC,decreasing=<span class=\"code-snippet__built_in\">T<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8ba1\u7b97\u57fa\u56e0\u7684logFC\uff08log2 fold change\uff09\u503c\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7528\u6765\u8861\u91cf\u5728\u9ad8\u8868\u8fbe\u7ec4\u4e0e\u4f4e\u8868\u8fbe\u7ec4\u4e4b\u95f4\u57fa\u56e0\u8868\u8fbe\u7684\u5dee\u5f02<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790GSEA\uff08Gene Set Enrichment Analysis\uff09\u6765\u8fdb\u884c\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u901a\u8fc7\u8c03\u7528GSEA\u51fd\u6570GSEA(logFC, TERM2GENE=gmt, nPerm=100, pvalueCutoff=1)\u6765\u6267\u884c\u5bcc\u96c6\u5206\u6790\uff0c\u5176\u4e2dlogFC\u662f\u57fa\u56e0\u7684logFC\u503c\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#TERM2GENE\u662f\u57fa\u56e0\u96c6\u6570\u636e\u5e93\uff0cnPerm\u662f\u968f\u673a\u91cd\u6392\u7684\u6b21\u6570\uff0cpvalueCutoff\u662f\u8bbe\u5b9a\u7684p\u503c\u9608\u503c\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">kk=GSEA(logFC,TERM2GENE=gmt, nPerm=<span class=\"code-snippet__number\">100<\/span>,pvalueCutoff = <span class=\"code-snippet__number\">1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">kkTab=as.data.frame(kk)<\/span><\/code><code><span class=\"code-snippet_outer\">kkTab=kkTab[kkTab$pvalue<<span class=\"code-snippet__number\">0.05<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\">write.table(kkTab,file=paste0(<span class=\"code-snippet__string\">\"Term.\"<\/span>,CancerType,<span class=\"code-snippet__string\">\".txt\"<\/span>),sep=<span class=\"code-snippet__string\">\"t\"<\/span>,<span class=\"code-snippet__built_in\">quote<\/span>=<span class=\"code-snippet__built_in\">F<\/span>,row.names = <span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u4fdd\u5b58\u4e3a\u4e00\u4e2a\u6570\u636e\u6846kkTab\uff0c\u5e76\u5c06p\u503c\u5c0f\u4e8e0.05\u7684\u5bcc\u96c6\u7ed3\u679c\u7b5b\u9009\u51fa\u6765\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u5199\u5165\u540d\u4e3a\"Term..txt\"\u7684\u6587\u672c\u6587\u4ef6\uff0c\u5176\u4e2dCancerType\u662f\u80bf\u7624\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u8f93\u51fa\u5bcc\u96c6\u7684\u56fe\u5f62<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6709\u81f3\u5c115\u4e2a\u5bcc\u96c6\u9879\uff0c\u5219\u8f93\u51fa\u524d5\u4e2a\u5bcc\u96c6\u56fe\u5f62\uff0c\u6bcf\u4e2a\u56fe\u5f62\u4fdd\u5b58\u4e3a\u4e00\u4e2aPDF\u6587\u4ef6\uff0c\u6587\u4ef6\u540d\u4e3a\"Term..pdf\"\uff0c<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5176\u4e2dCancerType\u662f\u80bf\u7624\u7c7b\u578b\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">termNum=<span class=\"code-snippet__number\">5<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span>(nrow(kkTab)>=termNum){<\/span><\/code><code><span class=\"code-snippet_outer\">gseaplot=gseaplot2(kk, row.names(kkTab)[<span class=\"code-snippet__number\">1<\/span>:termNum],base_size =<span class=\"code-snippet__number\">8<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pdf(file=paste0(<span class=\"code-snippet__string\">\"Term.\"<\/span>,CancerType,<span class=\"code-snippet__string\">\".pdf\"<\/span>),width=<span class=\"code-snippet__number\">8<\/span>,height=<span class=\"code-snippet__number\">6<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">print(gseaplot)<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 45.9582%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"3.4020100502512562\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_F0r3QS1a74VySic9z0Bx0SzduTI7gA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82dVzQ3xwt0dicJbqlObkzLVcPbUF0r3QS1a74VySic9z0Bx0SzduTI7gA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"199\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 100%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.55\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_wlFulrLlrr7YM7onynhLSiaic9XibQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb820582Eibcw9mheEO5FKibCnnyudCtSwlFulrLlrr7YM7onynhLSiaic9XibQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.7852112676056338\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_9hq1Tpe4H7SZYPeOIPDC19MY9zgX8w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82pOjNOvwdJ29BLQ2C1fRNXLA99hq1Tpe4H7SZYPeOIPDC19MY9zgX8w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"852\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.8284371327849589\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_85eklAIvTOPhwaJqYEYfXFFw2qfPIA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEUHD1uHnnibb36qDCOib9Zb82acdqelyKUOIiaicovmn33ULNl285eklAIvTOPhwaJqYEYfXFFw2qfPIA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"851\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-indent: 0em;white-space: normal;\">\u4ee5\u4e0a\u5c31\u662f\u5bf9\u7ed9\u5b9a\u7684\u80bf\u7624\u6570\u636e\uff0c\u4ee5\u53ca\u6307\u5b9a\u7684\u57fa\u56e0\u96c6\u6570\u636e\u5e93\uff08gmt\u6587\u4ef6\uff09\uff0c\u8fdb\u884c\u4e86\u57fa\u56e0\u96c6\u5bcc\u96c6\u5206\u6790\uff0c\u901a\u8fc7\u8f93\u51fa\u5bcc\u96c6\u5206\u6790\u7ed3\u679c\u7684\u6587\u672c\u6587\u4ef6\u548c\u5bcc\u96c6\u56fe\u5f62\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4e86\u89e3\u5728\u4e0d\u540c\u80bf\u7624\u7c7b\u578b\u4e2d\u4e0e<span style=\"text-indent: 0em;\">\u6307\u5b9a\u57fa\u56e0\u76f8\u5173\u7684\u751f\u7269\u5b66\u529f\u80fd\u548c\u901a\u8def\u3002<\/span><\/p>\n<p style=\"text-indent: 0em;white-space: normal;\"><span style=\"text-indent: 0em;\"><br \/><\/span><\/p>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"white-space: normal;\">\u4e0b\u671f\u5c06\u4e3a\u4f60\u5e26\u6765\u66f4\u591aR\u8bed\u8a00\u7684\u9a9a\u64cd\u4f5c\u6280\u5de7\uff0c\u4ee5\u4e0b\u63a8\u8350\u7684\u662f\u4e00\u4e2a\u591a\u529f\u80fd\u7684\u751f\u4fe1\u5e73\u53f0\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/p>\n<p style=\"white-space: normal;\">http:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n<p style=\"white-space: normal;\">\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/p>\n<p style=\"white-space: normal;\">http:\/\/www.biocloudservice.com\/home.html\u3002<\/p>\n<\/section>\n<section style=\"margin: 10px 0%;text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 40%;padding-right: 10px;align-self: center;flex: 0 0 auto;\">\n<section style=\"font-size: 6px;margin-right: 0%;margin-left: 0%;text-align: right;\" powered-by=\"xiumi.us\">\n<section 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