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0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4ec0\u4e48\u662fmaftools\uff1f<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;margin-bottom: 12px;text-wrap: wrap;\">maftools\u662f\u4e00\u4e2a\u5728R\u8bed\u8a00\u73af\u5883\u4e2d\u4f7f\u7528\u7684\u5f3a\u5927\u7684\u5de5\u5177\u5305\uff0c\u7528\u4e8e\u5206\u6790\u548c\u53ef\u89c6\u5316MAF\uff08Mutation Annotation Format\uff09\u6587\u4ef6\u3002MAF\u6587\u4ef6\u662f\u4e00\u79cd\u5e38\u7528\u7684\u5b58\u50a8\u80bf\u7624\u57fa\u56e0\u53d8\u5f02\u4fe1\u606f\u7684\u683c\u5f0f\u3002maftools\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\u548c\u56fe\u5f62\u5316\u5de5\u5177\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u80bf\u7624\u57fa\u56e0\u7ec4\u6570\u636e\u3002<\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4ee5\u4e0b\u662fmaftools\u5305\u7684\u4e00\u4e9b\u4e3b\u8981\u529f\u80fd\u548c\u7279\u70b9\uff1a<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1.\u8bfb\u53d6MAF\u6587\u4ef6<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86read.maf()\u51fd\u6570\uff0c\u65b9\u4fbf\u7528\u6237\u8bfb\u53d6\u548c\u89e3\u6790MAF\u6587\u4ef6\u3002\u5b83\u80fd\u591f\u81ea\u52a8\u5904\u7406\u4e0d\u540c\u7248\u672c\u7684MAF\u6587\u4ef6\uff0c\u5e76\u5c06\u5176\u8f6c\u6362\u4e3a\u6613\u4e8e\u5904\u7406\u7684\u6570\u636e\u7ed3\u6784\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>2.\u6570\u636e\u6458\u8981\u548c\u7edf\u8ba1<\/strong>\uff1amaftools\u5141\u8bb8\u7528\u6237\u5bf9MAF\u6587\u4ef6\u8fdb\u884c\u57fa\u672c\u7684\u6458\u8981\u548c\u7edf\u8ba1\u5206\u6790\u3002\u901a\u8fc7\u51fd\u6570\u5982mafSummary()\u548cmafStats()\uff0c\u53ef\u4ee5\u83b7\u53d6\u53d8\u5f02\u4f4d\u70b9\u7684\u5206\u5e03\u3001\u7a81\u53d8\u7c7b\u578b\u7684\u9891\u7387\u3001\u57fa\u56e0\u7ea7\u522b\u7684\u53d8\u5f02\u7edf\u8ba1\u7b49\u4fe1\u606f\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>3.\u53ef\u89c6\u5316\u5de5\u5177<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u76f4\u89c2\u5730\u5c55\u793a\u548c\u53ef\u89c6\u5316MAF\u6570\u636e\u3002\u4f8b\u5982\uff0concoplot()\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u57fa\u4e8e\u57fa\u56e0\u53d8\u5f02\u9891\u7387\u7684\u764c\u75c7\u7c7b\u578b\u6761\u5f62\u56fe\uff1boncostrip()\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u67d0\u4e9b\u5173\u6ce8\u57fa\u56e0\u7684\u7a81\u53d8\u6982\u51b5\uff1bplotTiTv()\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u78b1\u57fa\u8f6c\u6362\uff08Transition\uff09\u548c\u78b1\u57fa\u8f6c\u6362\uff08Transversion\uff09\u7684\u5206\u5e03\u6bd4\u4f8b\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>4.\u7a81\u53d8\u8d1f\u8377\u548c\u7a81\u53d8\u7279\u5f81\u5206\u6790<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\uff0c\u7528\u4e8e\u8bc4\u4f30\u80bf\u7624\u6837\u672c\u7684\u7a81\u53d8\u8d1f\u8377\uff08Mutation Burden\uff09\uff0c\u5305\u62ec\u7a81\u53d8\u6570\u76ee\u3001\u7a81\u53d8\u9891\u7387\u7b49\u7edf\u8ba1\u3002\u6b64\u5916\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7signatures()\u51fd\u6570\u6765\u8fdb\u884c\u7a81\u53d8\u7279\u5f81\u5206\u6790\uff0c\u8bc6\u522b\u6f5c\u5728\u7684\u7a81\u53d8\u6a21\u5f0f\u548c\u53d8\u5f02\u7279\u5f81\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>5.\u4ea4\u4e92\u5f0f\u53ef\u89c6\u5316\u548c\u62a5\u544a\u751f\u6210<\/strong>\uff1amaftools\u652f\u6301\u521b\u5efa\u4ea4\u4e92\u5f0f\u7684HTML\u62a5\u544a\uff0c\u5176\u4e2d\u5305\u542b\u4e86MAF\u6570\u636e\u7684\u6458\u8981\u4fe1\u606f\u3001\u7ed8\u56fe\u7ed3\u679c\u548c\u7edf\u8ba1\u5206\u6790\u7ed3\u679c\u3002\u8fd9\u4f7f\u5f97\u7528\u6237\u53ef\u4ee5\u65b9\u4fbf\u5730\u5171\u4eab\u548c\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u603b\u800c\u8a00\u4e4b\uff0cmaftools\u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u4e14\u6613\u4e8e\u4f7f\u7528\u7684R\u5305\uff0c\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e00\u5957\u5168\u9762\u7684\u5de5\u5177\uff0c\u5e2e\u52a9\u4ed6\u4eec\u5206\u6790\u548c\u7406\u89e3MAF\u6587\u4ef6\u4e2d\u7684\u80bf\u7624\u57fa\u56e0\u7ec4\u6570\u636e\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4e0b\u8f7dTCGA LIHC MAF \u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u597d\u5566\uff0c\u63a5\u4e0b\u6765\u8fdb\u5165\u6211\u4eec\u4eca\u5929\u7684\u6b63\u9898\uff0c\u9996\u5148\u6211\u4eec\u9700\u8981\u4e0b\u8f7dTCGA LUAD MAF\u6587\u4ef6\u3002\u6211\u4eec\u4eca\u5929\u901a\u8fc7TCGAbiolinks\u6765\u4e0b\u8f7d\u6240\u9700\u8981\u7684\u6570\u636e\uff0c\u6240\u4ee5\u5728\u4e0b\u8f7d\u4e4b\u524d\u5927\u5bb6\u8981\u786e\u4fdd\u5df2\u7ecf\u5b89\u88c5\u4e86TCGAbiolinks\u548cmaftools\u8fd9\u4e24\u4e2aR\u5305\u54e6\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">library(TCGAbiolinks)query <- GDCquery( project = <span class=\"code-snippet__string\">\"TCGA-LIHC\"<\/span>, data.category = <span class=\"code-snippet__string\">\"Simple Nucleotide Variation\"<\/span>, data.type = <span class=\"code-snippet__string\">\"Masked Somatic Mutation\"<\/span>, access = <span class=\"code-snippet__string\">\"open\"<\/span>)# \u4e0b\u8f7dGDCdownload(query)#\u4fdd\u5b58 \u8fd9\u91cc\u8981\u8bbe\u7f6e\u4e3a\u81ea\u5df1\u7684\u5de5\u4f5c\u76ee\u5f55<span class=\"code-snippet__meta\"># setwd(<span class=\"code-snippet__meta-string\">\"D:\/\u684c\u9762\/Rwork\/20221014\/TCGA_LUAD_maf\"<\/span>)setwd(<span class=\"code-snippet__meta-string\">\"\/media\/desk16\/iyun007\/maft1\"<\/span>)GDCprepare(query, save = T,save.filename = <span class=\"code-snippet__meta-string\">\"TCGA-LUAD_SNP.Rdata\"<\/span>)# \u8fd9\u91cc\u4e0b\u8f7d\u7684TCGA-LIHC_SNP.Rdata\u5c31\u662f\u6240\u9700\u8981\u7684maf\u6587\u4ef6\u4e86library(maftools)load(file = <span class=\"code-snippet__meta-string\">\".\/TCGA-LUAD_SNP.Rdata\"<\/span>) #\u52a0\u8f7d\u6b64\u6570\u636emaf.coad <- data# \u68c0\u67e5\u4e0b\u6570\u636eclass(maf.coad)dim(maf.coad)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4ee5\u4e0a\u4ee3\u7801\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u76f4\u63a5\u901a\u8fc7R\u5305\u4e0b\u8f7d\u597d\u6240\u9700\u7684\u6570\u636e\uff0c\u4ece\u800c\u514d\u4e8e\u4ece\u5b98\u65b9\u6570\u636e\u5e93\u4e0b\u8f7d\uff0c\u5f53\u7136\u540c\u5b66\u4eec\u4e5f\u53ef\u4ee5\u901a\u8fc7GDC\u6570\u636e\u5e93\u6765\u4e0b\u8f7d\u54e6\uff0c\u8be6\u7ec6\u7684\u4e0b\u8f7d\u65b9\u6cd5\u53c2\u89c1\u5c0f\u5e08\u59b9\u4e4b\u524d\u7684\u6559\u7a0b\u54e6\uff01<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>maftools\u5904\u7406TCGA\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u8bfb\u53d6MAF\u6570\u636e<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528read.maf()\u51fd\u6570\u8bfb\u53d6MAF\u6570\u636e\u6587\u4ef6\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728\u53d8\u91cflaml\u4e2d\u3002\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u53ea\u8bfb\u53d6\u7ec4\u5b66\u6570\u636e\uff0c\u4e0d\u6dfb\u52a0\u4e34\u5e8a\u6570\u636e\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u8bfb\u53d6maf\u6587\u4ef6library(maftools)laml <- read.maf(maf.code)#\u672c\u6b21\u53ea\u5c55\u793amaf\u7684\u4e00\u4e9b\u7edf\u8ba1\u7ed8\u56fe\uff0c\u53ea\u8bfb\u5165\u7ec4\u5b66\u6570\u636e\uff0c\u4e0d\u6dfb\u52a0\u4e34\u5e8a\u6570\u636e<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u67e5\u770b\u6570\u636e\u57fa\u672c\u60c5\u51b5<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528laml\u6765\u67e5\u770b\u8bfb\u53d6\u7684MAF\u6570\u636e\u7684\u57fa\u672c\u60c5\u51b5\uff0c\u5305\u62ec\u6570\u636e\u6458\u8981\u548c\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#laml = read.maf(maf = laml.maf)#\u67e5\u770b\u6570\u636e\u7684\u57fa\u672c\u60c5\u51b5lamlwrite.mafSummary(maf = laml, basename = <span class=\"code-snippet__meta-string\">'laml'<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236MAF\u6587\u4ef6\u7684\u6574\u4f53\u7ed3\u679c\u56fe<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">plotmafSummary(maf = maf1, rmOutlier = TRUE, addStat = <span class=\"code-snippet__string\">'median'<\/span>, dashboard = TRUE)<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0009910802775024\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_6f8GuAvJsHb7ZNibTVT5nVZqPIjrFw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibu2mt8rnJvGtVWkkt1zlOWnAfw36f8GuAvJsHb7ZNibTVT5nVZqPIjrFw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1009\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236oncoplot\u56fe<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#oncoplot for top 20 genes.oncoplot(maf = laml, top = 20)<\/span><\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9916666666666667\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_KU2DUPFlKzibhEybZJr2HOKFquJiaw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuGjf8bic5uaGVr5eIkXHkr1ibqr2sKU2DUPFlKzibhEybZJr2HOKFquJiaw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236Oncostrip\u56fe<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u53ef\u4ee5\u4f7f\u7528 oncostrip \u51fd\u6570\u5c55\u793a\u7279\u5b9a\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u7684\u7a81\u53d8\u60c5\u51b5\uff0c\u6b64\u5904\u67e5\u770b\u809d\u764c\u4e2d\u5173\u6ce8\u8f83\u591a\u7684’TP53′,’CTNNB1′, ‘ARID1A’\u4e09\u4e2a\u57fa\u56e0\uff0c\u5982\u4e0b\uff1a<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">oncostrip(maf = laml, genes = c(<span class=\"code-snippet__string\">'TP53'<\/span>,<span class=\"code-snippet__string\">'CTNNB1'<\/span>, <span class=\"code-snippet__string\">'ARID1A'<\/span>))<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9603567888999008\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_82FPyDysrDwBVkcrrcOzehyHIUic8w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibu3OH0menvMVLsrDI46ZntSNuqc82FPyDysrDwBVkcrrcOzehyHIUic8w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1009\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">Transition vs Transversions<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">titv\u51fd\u6570\u5c06SNP\u5206\u7c7b\u4e3aTransitions_vs_Transversions\uff0c\u5e76\u4ee5\u5404\u79cd\u65b9\u5f0f\u8fd4\u56de\u6c47\u603b\u8868\u7684\u5217\u8868\u3002\u6c47\u603b\u6570\u636e\u4e5f\u53ef\u4ee5\u663e\u793a\u4e3a\u4e00\u4e2a\u7bb1\u7ebf\u56fe\u5806\u79ef\u6761\u5f62\u56fe\u663e\u793a\u6bcf\u4e2a\u6837\u672c\u4e2d\u7684\u8f6c\u6362\u6bd4\u4f8b<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">laml.titv = titv(maf = laml, plot = FALSE, useSyn = TRUE)<span class=\"code-snippet__meta\">#plot titv summaryplotTiTv(res = laml.titv)<\/span><\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0009940357852882\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_zKvGxSd0r9Dx2b1e0OctmQZ0EFxGRQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuAASqiavYDzPGxggp4iaHI3pSsazKvGxSd0r9Dx2b1e0OctmQZ0EFxGRQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1006\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">Rainfall plots<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528rainfallPlot\u53c2\u6570\u7ed8\u5236rainfall plots\uff0c\u5c55\u793a\u8d85\u7a81\u53d8\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u3002detectChangePoints\u8bbe\u7f6e\u4e3aTRUE\uff0crainfall plots\u53ef\u4ee5\u7a81\u51fa\u663e\u793a\u6f5c\u5728\u53d8\u5316\u7684\u533a\u57df\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">rainfallPlot(maf = laml, detectChangePoints = TRUE, pointSize = <span class=\"code-snippet__number\">0.6<\/span>)<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9398797595190381\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_ersymM0w8N485GCEHWSK7TceDmib1Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuqyWFia34zhtU3XblQw1FGx5n4qersymM0w8N485GCEHWSK7TceDmib1Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"998\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;margin-bottom: 12px;text-wrap: wrap;\">\u901a\u8fc7\u4ee5\u4e0a\u6b65\u9aa4\uff0c\u4f60\u53ef\u4ee5\u4f7f\u7528\u7ed9\u5b9a\u7684\u4ee3\u7801\u4e0b\u8f7dTCGA\u7684MAF\u6570\u636e\u5e76\u8fdb\u884c\u57fa\u672c\u7684\u6570\u636e\u6574\u7406\u548c\u5206\u6790\u3002\u5c0f\u5e08\u59b9\u6e29\u99a8\u63d0\u793a\uff1a\u4e00\u5b9a\u8981\u786e\u4fdd\u5728\u8fd0\u884c\u4ee3\u7801\u4e4b\u524d\uff0c\u786e\u4fdd\u6b63\u786e\u5b89\u88c5\u4e86\u6240\u9700\u7684R\u5305\uff0c\u5e76\u6839\u636e\u9700\u8981\u4fee\u6539\u6587\u4ef6\u8def\u5f84\u548c\u5176\u4ed6\u53c2\u6570\u54e6\u3002<\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u600e\u4e48\u6837\uff0c\u4eca\u5929\u7684\u6559\u7a0b\u4f60\u5b66\u4f1a\u4e86\u5417\uff1f\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff01\u66f4\u591a\u5b66\u4e60\u5e72\u8d27\u8bf7\u7ee7\u7eed\u5173\u6ce8\u5c0f\u5e08\u59b9\u54e6\uff01<\/p>\n<p><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\/7_akXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ-10.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><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3575547866205306\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_HVzeSsosMjColwxeR2aMsicmMgicVQ.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEUEOPhTDbhztaU7davdEP2YwrJAkVkEBJERQsIkEkqD5wX4VcHVzeSsosMjColwxeR2aMsicmMgicVQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"867\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\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=\"https:\/\/v.xiumi.us\/board\/v5\/6rNpH\/476214153\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/v.xiumi.us\/board\/v5\/6rNpH\/476214153\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u73a9\u8f6cmaftools\uff1a\u63a2\u7d22TCGA\u7684\u57fa\u56e0\u4e16\u754c\uff01 \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c 2 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{"id":59556,"date":"2024-06-17T08:28:52","date_gmt":"2024-06-17T00:28:52","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59556"},"modified":"2024-06-17T08:28:52","modified_gmt":"2024-06-17T00:28:52","slug":"%e7%8e%a9%e8%bd%acmaftools%ef%bc%9a%e6%8e%a2%e7%b4%a2tcga%e7%9a%84%e5%9f%ba%e5%9b%a0%e4%b8%96%e7%95%8c%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=59556","title":{"rendered":"\u73a9\u8f6cmaftools\uff1a\u63a2\u7d22TCGA\u7684\u57fa\u56e0\u4e16\u754c\uff01"},"content":{"rendered":"

\n
\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">hello\uff0c\u4f60\u77e5\u9053\u5982\u4f55\u4f7f\u7528maftools\u5904\u7406TCGA\u6570\u636e\u5e93\u4e0b\u8f7d\u7684maf\u6587\u4ef6\u5417\uff1f\u4eca\u5929\u5c0f\u5e08\u59b9\u5c31\u6765\u6559\u4f60\u8f7b\u677e\u5b9e\u73b0\uff01\u5e26\u4f60\u73a9\u8f6cmaftools\u5305\uff0c\u611f\u5174\u8da3\u7684\u8bdd\u5c31\u548c\u5c0f\u5e08\u59b9\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;\" 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-backh=\"109\" data-backw=\"109\" data-ratio=\"1\" data-s=\"300,640\" 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0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4ec0\u4e48\u662fmaftools\uff1f<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;margin-bottom: 12px;text-wrap: wrap;\">maftools\u662f\u4e00\u4e2a\u5728R\u8bed\u8a00\u73af\u5883\u4e2d\u4f7f\u7528\u7684\u5f3a\u5927\u7684\u5de5\u5177\u5305\uff0c\u7528\u4e8e\u5206\u6790\u548c\u53ef\u89c6\u5316MAF\uff08Mutation Annotation Format\uff09\u6587\u4ef6\u3002MAF\u6587\u4ef6\u662f\u4e00\u79cd\u5e38\u7528\u7684\u5b58\u50a8\u80bf\u7624\u57fa\u56e0\u53d8\u5f02\u4fe1\u606f\u7684\u683c\u5f0f\u3002maftools\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\u548c\u56fe\u5f62\u5316\u5de5\u5177\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u66f4\u597d\u5730\u7406\u89e3\u548c\u89e3\u91ca\u80bf\u7624\u57fa\u56e0\u7ec4\u6570\u636e\u3002<\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4ee5\u4e0b\u662fmaftools\u5305\u7684\u4e00\u4e9b\u4e3b\u8981\u529f\u80fd\u548c\u7279\u70b9\uff1a<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><strong>1.\u8bfb\u53d6MAF\u6587\u4ef6<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86read.maf()\u51fd\u6570\uff0c\u65b9\u4fbf\u7528\u6237\u8bfb\u53d6\u548c\u89e3\u6790MAF\u6587\u4ef6\u3002\u5b83\u80fd\u591f\u81ea\u52a8\u5904\u7406\u4e0d\u540c\u7248\u672c\u7684MAF\u6587\u4ef6\uff0c\u5e76\u5c06\u5176\u8f6c\u6362\u4e3a\u6613\u4e8e\u5904\u7406\u7684\u6570\u636e\u7ed3\u6784\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>2.\u6570\u636e\u6458\u8981\u548c\u7edf\u8ba1<\/strong>\uff1amaftools\u5141\u8bb8\u7528\u6237\u5bf9MAF\u6587\u4ef6\u8fdb\u884c\u57fa\u672c\u7684\u6458\u8981\u548c\u7edf\u8ba1\u5206\u6790\u3002\u901a\u8fc7\u51fd\u6570\u5982mafSummary()\u548cmafStats()\uff0c\u53ef\u4ee5\u83b7\u53d6\u53d8\u5f02\u4f4d\u70b9\u7684\u5206\u5e03\u3001\u7a81\u53d8\u7c7b\u578b\u7684\u9891\u7387\u3001\u57fa\u56e0\u7ea7\u522b\u7684\u53d8\u5f02\u7edf\u8ba1\u7b49\u4fe1\u606f\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>3.\u53ef\u89c6\u5316\u5de5\u5177<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86\u591a\u79cd\u7ed8\u56fe\u51fd\u6570\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u76f4\u89c2\u5730\u5c55\u793a\u548c\u53ef\u89c6\u5316MAF\u6570\u636e\u3002\u4f8b\u5982\uff0concoplot()\u51fd\u6570\u53ef\u4ee5\u751f\u6210\u57fa\u4e8e\u57fa\u56e0\u53d8\u5f02\u9891\u7387\u7684\u764c\u75c7\u7c7b\u578b\u6761\u5f62\u56fe\uff1boncostrip()\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u67d0\u4e9b\u5173\u6ce8\u57fa\u56e0\u7684\u7a81\u53d8\u6982\u51b5\uff1bplotTiTv()\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u78b1\u57fa\u8f6c\u6362\uff08Transition\uff09\u548c\u78b1\u57fa\u8f6c\u6362\uff08Transversion\uff09\u7684\u5206\u5e03\u6bd4\u4f8b\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>4.\u7a81\u53d8\u8d1f\u8377\u548c\u7a81\u53d8\u7279\u5f81\u5206\u6790<\/strong>\uff1amaftools\u63d0\u4f9b\u4e86\u4e00\u7cfb\u5217\u51fd\u6570\uff0c\u7528\u4e8e\u8bc4\u4f30\u80bf\u7624\u6837\u672c\u7684\u7a81\u53d8\u8d1f\u8377\uff08Mutation Burden\uff09\uff0c\u5305\u62ec\u7a81\u53d8\u6570\u76ee\u3001\u7a81\u53d8\u9891\u7387\u7b49\u7edf\u8ba1\u3002\u6b64\u5916\uff0c\u4e5f\u53ef\u4ee5\u901a\u8fc7signatures()\u51fd\u6570\u6765\u8fdb\u884c\u7a81\u53d8\u7279\u5f81\u5206\u6790\uff0c\u8bc6\u522b\u6f5c\u5728\u7684\u7a81\u53d8\u6a21\u5f0f\u548c\u53d8\u5f02\u7279\u5f81\u3002<\/p>\n<p><br \/><\/p>\n<p><strong>5.\u4ea4\u4e92\u5f0f\u53ef\u89c6\u5316\u548c\u62a5\u544a\u751f\u6210<\/strong>\uff1amaftools\u652f\u6301\u521b\u5efa\u4ea4\u4e92\u5f0f\u7684HTML\u62a5\u544a\uff0c\u5176\u4e2d\u5305\u542b\u4e86MAF\u6570\u636e\u7684\u6458\u8981\u4fe1\u606f\u3001\u7ed8\u56fe\u7ed3\u679c\u548c\u7edf\u8ba1\u5206\u6790\u7ed3\u679c\u3002\u8fd9\u4f7f\u5f97\u7528\u6237\u53ef\u4ee5\u65b9\u4fbf\u5730\u5171\u4eab\u548c\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u603b\u800c\u8a00\u4e4b\uff0cmaftools\u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u4e14\u6613\u4e8e\u4f7f\u7528\u7684R\u5305\uff0c\u4e3a\u7814\u7a76\u4eba\u5458\u63d0\u4f9b\u4e86\u4e00\u5957\u5168\u9762\u7684\u5de5\u5177\uff0c\u5e2e\u52a9\u4ed6\u4eec\u5206\u6790\u548c\u7406\u89e3MAF\u6587\u4ef6\u4e2d\u7684\u80bf\u7624\u57fa\u56e0\u7ec4\u6570\u636e\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>\u4e0b\u8f7dTCGA LIHC MAF \u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u597d\u5566\uff0c\u63a5\u4e0b\u6765\u8fdb\u5165\u6211\u4eec\u4eca\u5929\u7684\u6b63\u9898\uff0c\u9996\u5148\u6211\u4eec\u9700\u8981\u4e0b\u8f7dTCGA LUAD MAF\u6587\u4ef6\u3002\u6211\u4eec\u4eca\u5929\u901a\u8fc7TCGAbiolinks\u6765\u4e0b\u8f7d\u6240\u9700\u8981\u7684\u6570\u636e\uff0c\u6240\u4ee5\u5728\u4e0b\u8f7d\u4e4b\u524d\u5927\u5bb6\u8981\u786e\u4fdd\u5df2\u7ecf\u5b89\u88c5\u4e86TCGAbiolinks\u548cmaftools\u8fd9\u4e24\u4e2aR\u5305\u54e6\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">library(TCGAbiolinks)query <- GDCquery( project = <span class=\"code-snippet__string\">\"TCGA-LIHC\"<\/span>, data.category = <span class=\"code-snippet__string\">\"Simple Nucleotide Variation\"<\/span>, data.type = <span class=\"code-snippet__string\">\"Masked Somatic Mutation\"<\/span>, access = <span class=\"code-snippet__string\">\"open\"<\/span>)# \u4e0b\u8f7dGDCdownload(query)#\u4fdd\u5b58 \u8fd9\u91cc\u8981\u8bbe\u7f6e\u4e3a\u81ea\u5df1\u7684\u5de5\u4f5c\u76ee\u5f55<span class=\"code-snippet__meta\"># setwd(<span class=\"code-snippet__meta-string\">\"D:\/\u684c\u9762\/Rwork\/20221014\/TCGA_LUAD_maf\"<\/span>)setwd(<span class=\"code-snippet__meta-string\">\"\/media\/desk16\/iyun007\/maft1\"<\/span>)GDCprepare(query, save = T,save.filename = <span class=\"code-snippet__meta-string\">\"TCGA-LUAD_SNP.Rdata\"<\/span>)# \u8fd9\u91cc\u4e0b\u8f7d\u7684TCGA-LIHC_SNP.Rdata\u5c31\u662f\u6240\u9700\u8981\u7684maf\u6587\u4ef6\u4e86library(maftools)load(file = <span class=\"code-snippet__meta-string\">\".\/TCGA-LUAD_SNP.Rdata\"<\/span>) #\u52a0\u8f7d\u6b64\u6570\u636emaf.coad <- data# \u68c0\u67e5\u4e0b\u6570\u636eclass(maf.coad)dim(maf.coad)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4ee5\u4e0a\u4ee3\u7801\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u76f4\u63a5\u901a\u8fc7R\u5305\u4e0b\u8f7d\u597d\u6240\u9700\u7684\u6570\u636e\uff0c\u4ece\u800c\u514d\u4e8e\u4ece\u5b98\u65b9\u6570\u636e\u5e93\u4e0b\u8f7d\uff0c\u5f53\u7136\u540c\u5b66\u4eec\u4e5f\u53ef\u4ee5\u901a\u8fc7GDC\u6570\u636e\u5e93\u6765\u4e0b\u8f7d\u54e6\uff0c\u8be6\u7ec6\u7684\u4e0b\u8f7d\u65b9\u6cd5\u53c2\u89c1\u5c0f\u5e08\u59b9\u4e4b\u524d\u7684\u6559\u7a0b\u54e6\uff01<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"text-align: center;justify-content: center;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: left;transform: translate3d(-20px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"justify-content: center;display: flex;flex-flow: row;margin-top: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: auto;align-self: center;flex: 0 0 auto;min-width: 5%;height: auto;padding-right: 17px;padding-left: 17px;\">\n<section style=\"font-size: 24px;\" powered-by=\"xiumi.us\">\n<p><strong>maftools\u5904\u7406TCGA\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: middle;width: 30px;align-self: center;flex: 0 0 auto;height: auto;background-color: rgb(212, 215, 165);line-height: 0;padding-top: 6px;padding-bottom: 6px;overflow: hidden;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: 0.5em;margin-bottom: 0.5em;text-align: right;transform: translate3d(24px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"background-color: rgb(143, 146, 85);height: 1px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u8bfb\u53d6MAF\u6570\u636e<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528read.maf()\u51fd\u6570\u8bfb\u53d6MAF\u6570\u636e\u6587\u4ef6\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u50a8\u5728\u53d8\u91cflaml\u4e2d\u3002\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u53ea\u8bfb\u53d6\u7ec4\u5b66\u6570\u636e\uff0c\u4e0d\u6dfb\u52a0\u4e34\u5e8a\u6570\u636e\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">#\u8bfb\u53d6maf\u6587\u4ef6library(maftools)laml <- read.maf(maf.code)#\u672c\u6b21\u53ea\u5c55\u793amaf\u7684\u4e00\u4e9b\u7edf\u8ba1\u7ed8\u56fe\uff0c\u53ea\u8bfb\u5165\u7ec4\u5b66\u6570\u636e\uff0c\u4e0d\u6dfb\u52a0\u4e34\u5e8a\u6570\u636e<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u67e5\u770b\u6570\u636e\u57fa\u672c\u60c5\u51b5<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528laml\u6765\u67e5\u770b\u8bfb\u53d6\u7684MAF\u6570\u636e\u7684\u57fa\u672c\u60c5\u51b5\uff0c\u5305\u62ec\u6570\u636e\u6458\u8981\u548c\u7edf\u8ba1\u4fe1\u606f\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#laml = read.maf(maf = laml.maf)#\u67e5\u770b\u6570\u636e\u7684\u57fa\u672c\u60c5\u51b5lamlwrite.mafSummary(maf = laml, basename = <span class=\"code-snippet__meta-string\">'laml'<\/span>)<\/span><\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236MAF\u6587\u4ef6\u7684\u6574\u4f53\u7ed3\u679c\u56fe<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">plotmafSummary(maf = maf1, rmOutlier = TRUE, addStat = <span class=\"code-snippet__string\">'median'<\/span>, dashboard = TRUE)<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0009910802775024\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_6f8GuAvJsHb7ZNibTVT5nVZqPIjrFw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibu2mt8rnJvGtVWkkt1zlOWnAfw36f8GuAvJsHb7ZNibTVT5nVZqPIjrFw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1009\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236oncoplot\u56fe<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#oncoplot for top 20 genes.oncoplot(maf = laml, top = 20)<\/span><\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9916666666666667\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_KU2DUPFlKzibhEybZJr2HOKFquJiaw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuGjf8bic5uaGVr5eIkXHkr1ibqr2sKU2DUPFlKzibhEybZJr2HOKFquJiaw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">\u7ed8\u5236Oncostrip\u56fe<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u53ef\u4ee5\u4f7f\u7528 oncostrip \u51fd\u6570\u5c55\u793a\u7279\u5b9a\u57fa\u56e0\u5728\u6837\u672c\u4e2d\u7684\u7a81\u53d8\u60c5\u51b5\uff0c\u6b64\u5904\u67e5\u770b\u809d\u764c\u4e2d\u5173\u6ce8\u8f83\u591a\u7684’TP53′,’CTNNB1′, ‘ARID1A’\u4e09\u4e2a\u57fa\u56e0\uff0c\u5982\u4e0b\uff1a<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">oncostrip(maf = laml, genes = c(<span class=\"code-snippet__string\">'TP53'<\/span>,<span class=\"code-snippet__string\">'CTNNB1'<\/span>, <span class=\"code-snippet__string\">'ARID1A'<\/span>))<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9603567888999008\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_82FPyDysrDwBVkcrrcOzehyHIUic8w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibu3OH0menvMVLsrDI46ZntSNuqc82FPyDysrDwBVkcrrcOzehyHIUic8w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1009\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">Transition vs Transversions<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">titv\u51fd\u6570\u5c06SNP\u5206\u7c7b\u4e3aTransitions_vs_Transversions\uff0c\u5e76\u4ee5\u5404\u79cd\u65b9\u5f0f\u8fd4\u56de\u6c47\u603b\u8868\u7684\u5217\u8868\u3002\u6c47\u603b\u6570\u636e\u4e5f\u53ef\u4ee5\u663e\u793a\u4e3a\u4e00\u4e2a\u7bb1\u7ebf\u56fe\u5806\u79ef\u6761\u5f62\u56fe\u663e\u793a\u6bcf\u4e2a\u6837\u672c\u4e2d\u7684\u8f6c\u6362\u6bd4\u4f8b<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">laml.titv = titv(maf = laml, plot = FALSE, useSyn = TRUE)<span class=\"code-snippet__meta\">#plot titv summaryplotTiTv(res = laml.titv)<\/span><\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0009940357852882\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_zKvGxSd0r9Dx2b1e0OctmQZ0EFxGRQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuAASqiavYDzPGxggp4iaHI3pSsazKvGxSd0r9Dx2b1e0OctmQZ0EFxGRQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1006\" style=\"vertical-align: middle;width: 100%;display: inline;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><span style=\"font-size: 20px;text-decoration: underline;\">Rainfall plots<\/span><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u4f7f\u7528rainfallPlot\u53c2\u6570\u7ed8\u5236rainfall plots\uff0c\u5c55\u793a\u8d85\u7a81\u53d8\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u3002detectChangePoints\u8bbe\u7f6e\u4e3aTRUE\uff0crainfall plots\u53ef\u4ee5\u7a81\u51fa\u663e\u793a\u6f5c\u5728\u53d8\u5316\u7684\u533a\u57df\u3002<\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">rainfallPlot(maf = laml, detectChangePoints = TRUE, pointSize = <span class=\"code-snippet__number\">0.6<\/span>)<\/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;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.9398797595190381\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_ersymM0w8N485GCEHWSK7TceDmib1Q.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/oCSOtP61aEWtNKoZ5Q9WPpeCW7k3cBibuqyWFia34zhtU3XblQw1FGx5n4qersymM0w8N485GCEHWSK7TceDmib1Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"998\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;align-self: flex-start;flex: 100 100 0%;height: auto;background-color: rgb(247, 247, 237);padding: 28px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p style=\"text-indent: 2em;margin-bottom: 12px;text-wrap: wrap;\">\u901a\u8fc7\u4ee5\u4e0a\u6b65\u9aa4\uff0c\u4f60\u53ef\u4ee5\u4f7f\u7528\u7ed9\u5b9a\u7684\u4ee3\u7801\u4e0b\u8f7dTCGA\u7684MAF\u6570\u636e\u5e76\u8fdb\u884c\u57fa\u672c\u7684\u6570\u636e\u6574\u7406\u548c\u5206\u6790\u3002\u5c0f\u5e08\u59b9\u6e29\u99a8\u63d0\u793a\uff1a\u4e00\u5b9a\u8981\u786e\u4fdd\u5728\u8fd0\u884c\u4ee3\u7801\u4e4b\u524d\uff0c\u786e\u4fdd\u6b63\u786e\u5b89\u88c5\u4e86\u6240\u9700\u7684R\u5305\uff0c\u5e76\u6839\u636e\u9700\u8981\u4fee\u6539\u6587\u4ef6\u8def\u5f84\u548c\u5176\u4ed6\u53c2\u6570\u54e6\u3002<\/p>\n<p style=\"text-indent: 2em;text-wrap: wrap;\">\u600e\u4e48\u6837\uff0c\u4eca\u5929\u7684\u6559\u7a0b\u4f60\u5b66\u4f1a\u4e86\u5417\uff1f\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff01\u66f4\u591a\u5b66\u4e60\u5e72\u8d27\u8bf7\u7ee7\u7eed\u5173\u6ce8\u5c0f\u5e08\u59b9\u54e6\uff01<\/p>\n<p><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\/7_akXKU5NcO1KwuWc1Rk7ZJ56LC2pYrQ-10.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><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3575547866205306\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_HVzeSsosMjColwxeR2aMsicmMgicVQ.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/oCSOtP61aEUEOPhTDbhztaU7davdEP2YwrJAkVkEBJERQsIkEkqD5wX4VcHVzeSsosMjColwxeR2aMsicmMgicVQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"867\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: top;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;padding-left: 21px;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\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=\"https:\/\/v.xiumi.us\/board\/v5\/6rNpH\/476214153\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"https:\/\/v.xiumi.us\/board\/v5\/6rNpH\/476214153\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u73a9\u8f6cmaftools\uff1a\u63a2\u7d22TCGA\u7684\u57fa\u56e0\u4e16\u754c\uff01 \u5c0f\u5e08\u59b9 \u751f\u4fe1\u679c 2 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