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TMB\uff09\uff0c\u800c\u8981\u60f3\u753b\u51fa\u8fd9\u5f20\u56fe\uff0c\u9996\u5148\u6211\u4eec\u5fc5\u987b\u8981\u51c6\u672c\u597d\u6570\u636e\u3002\u4eca\u5929\u5927\u6d77\u54e5\u5c31\u5148\u6765\u8ddf\u5927\u5bb6\u804a\u804a\u600e\u4e48\u4eceTCGA\u6570\u636e\u5e93\u4e0b\u8f7d\u4f53\u7ec6\u80de\u7a81\u53d8\u6570\u636e\u5e76\u8ba1\u7b97TMB\u503c\u3002<\/p>\n<p>\u9996\u5148\u6211\u4eec\u5148\u8fdb\u5165TCGA\u6570\u636e\u5e93\u4e3b\u9875\uff08https:\/\/portal.gdc.cancer.gov\/\uff09\u3002\u7136\u540e\u5c31\u53ef\u4ee5\u5728\u641c\u7d22\u6846\u4e2d\u8f93\u5165\u6211\u4eec\u611f\u5174\u8da3\u7684\u764c\u75c7ID\uff0c\u5982\u4e0b\u56fe\u6807\u8bb0\u6240\u793a\uff0c\u5927\u6d77\u54e5\u5c31\u7528\u5e38\u89c1\u7684\u80ba\u764c\u6570\u636e\u4e3a\u4f8b\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.45740740740740743\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/2_g009aMERR3nqSGcCAD8bdK1vsSiaXA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1rXWuDqKTJq2f9h7CUzCh0zN65g009aMERR3nqSGcCAD8bdK1vsSiaXA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u6211\u4eec\u70b9\u51fb\u4e0a\u9762\u7684\u68c0\u7d22\u63a8\u8350\u7b2c\u4e00\u4e2a\uff0c\u4f1a\u51fa\u73b0\u4e0b\u9762\u7684\u641c\u7d22\u7ed3\u679c\u9875\u9762\uff0c\u7136\u540e\u6211\u4eec\u70b9\u51fb\u56fe\u793a\u7684\u7ea2\u8272\u6807\u8bb0\u5904\u7684Simple Nucleotide Variation\u7684\u540e\u9762\u7684571\u4f8bcase\u5904<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.4564814814814815\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/3_xUpnVoWib95hYiaYM595K8KIAad8HA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1riciawu9wBhicVhYh35KlpY21iaRLsxUpnVoWib95hYiaYM595K8KIAad8HA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u70b9\u8fdb\u53bb\u540e\uff0c\u6211\u4eec\u53d1\u73b0\u6709\u7740\u5f88\u591a\u79cd\u7c7b\u7684\u6570\u636e\uff0c\u7136\u540e\u6211\u4eec\u9700\u8981\u4e00\u6b65\u4e00\u6b65\u7b5b\u9009\u51fa\u6211\u4eec\u9700\u8981\u7684\u7a81\u53d8\u6570\u636e\uff0c\u9700\u8981\u5927\u5bb6\u6309\u4e0b\u56fe\u6807\u8bb0\u52fe\u9009\uff0c\u5148\u70b9\u51fbFiles\uff0c\u52fe\u9009\u4e0asimple nucleotide variation\u3001Masked Somatic Mutation\u3001WXS\u3001maf\u3001open\u7b49\u9009\u9879\uff0c\u4e00\u4e2a\u90fd\u4e0d\u53ef\u4ee5\u6f0f\u54e6\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.4527777777777778\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/4_5PzA3HhfkzAibWQVqfAoIfAicibp0Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1tTph0mpXYaohnrS09jSx6QWxAy75PzA3HhfkzAibWQVqfAoIfAicibp0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u5269\u4f59\u7684\u7ed3\u679c\u5c31\u662f\u6211\u4eec\u9700\u8981\u7684\u6570\u636e\uff0c\u63a5\u7740\u6211\u4eec\u9009\u62e9Case\uff0c\u70b9\u51fbAdd all Files to Cart\uff0c<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.4601851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_9TEdyYoxhziablxI2AMTmTWRasH5yw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1JFp0IBVmrLDomCGX4f7WgrpCS9TEdyYoxhziablxI2AMTmTWRasH5yw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u968f\u540e\u70b9\u51fb\u53f3\u4e0a\u89d2\u7684Cart\uff0c\u8fdb\u53bb\u540e\uff0c\u76f4\u63a5\u4e0b\u8f7d\uff0c\u9009\u62e9Cart\u5c31\u53ef\u4ee5\u5566\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3398148148148148\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/6_xLK7ibY9VpUiaYEazMFCAl0qATdruw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C11Cjn17FBib2nXM1pXxeCFxcSbcAxLK7ibY9VpUiaYEazMFCAl0qATdruw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a\u538b\u7f29\u5305\uff0c\u6211\u4eec\u9700\u8981\u628a\u5b83\u89e3\u538b\u653e\u5728\u6587\u4ef6\u5939\u4e2d\uff0c\u4f1a\u5f97\u5230\u5982\u56fe\u7684\u6587\u4ef6<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.7351851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_V6NG68fx8lvdLFzKXcNqIxwVBS7uag.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1Q6bWAsgpzUfkKTYibQwbVF2kLV6NG68fx8lvdLFzKXcNqIxwVBS7uag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u770b\u7740\u8fd9\u4e48\u591a\u6587\u4ef6\u5939\uff0c\u5f88\u591a\u5c0f\u4f19\u4f34\u80af\u5b9a\u61f5\u4e86\uff0c\u8fd9\u600e\u4e48\u5904\u7406\uff0c\u624b\u52a8\u6574\u5408\uff1f\u60f3\u60f3\u90fd\u5bb3\u6015\uff01\u522b\u62c5\u5fc3\uff0c\u5927\u6d77\u54e5\u6765\u5e2e\u4f60\uff0c\u7528\u4ee3\u7801\u4e00\u952e\u89e3\u51b3\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5148\u8bbe\u5b9a\u5de5\u4f5c\u76ee\u5f55\uff0c\u5c31\u8bbe\u7f6e\u4e3a\u89e3\u538b\u540e\u7684\u8def\u5f84<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">setwd(<span class=\"code-snippet__string\">\"C:\/Users\/Administrator\/Desktop\/gdc\/ gdc_download_20230809_022518.121743\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bfc\u5165\u4e24\u4e2a\u5173\u952e\u7684R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(maftools)<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u83b7\u53d6\u6240\u6709\u7684\u538b\u7f29\u6587\u4ef6\uff0c\u8fd9\u4e00\u6b65\u53ef\u80fd\u4f1a\u9700\u8981\u4e00\u4e9b\u65f6\u95f4\uff0c\u53d6\u51b3\u4e8e\u6211\u4eec\u7814\u7a76\u7684\u764c\u75c7\u6837\u672c\u89c4\u6a21\u5927\u5c0f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">files <- list.files(pattern = <span class=\"code-snippet__string\">'*.gz'<\/span>,recursive = <span class=\"code-snippet__literal\">TRUE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">all_mut <- data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (file <span class=\"code-snippet__keyword\">in<\/span> files) {<\/span><\/code><code><span class=\"code-snippet_outer\"> mut <- read.delim(file,skip = <span class=\"code-snippet__number\">7<\/span>, header = <span class=\"code-snippet__built_in\">T<\/span>, fill = <span class=\"code-snippet__literal\">TRUE<\/span>,sep = <span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> all_mut <- rbind(all_mut,mut)<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6570\u636e\u6574\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">all_mut <- read.maf(all_mut)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">a <- all_mut@data %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> .[,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Hugo_Symbol\"<\/span>,<span class=\"code-snippet__string\">\"Variant_Classification\"<\/span>,<span class=\"code-snippet__string\">\"Tumor_Sample_Barcode\"<\/span>)] %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> as.data.frame() %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> mutate(Tumor_Sample_Barcode = substring(.$Tumor_Sample_Barcode,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">12<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">gene <- <span class=\"code-snippet__built_in\">as.character<\/span>(unique(a$Hugo_Symbol))<\/span><\/code><code><span class=\"code-snippet_outer\">sample <- <span class=\"code-snippet__built_in\">as.character<\/span>(unique(a$Tumor_Sample_Barcode))<\/span><\/code><code><span class=\"code-snippet_outer\">mat <- as.data.frame(matrix(<span class=\"code-snippet__string\">\"\"<\/span>,<span class=\"code-snippet__built_in\">length<\/span>(gene),<span class=\"code-snippet__built_in\">length<\/span>(sample),<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">dimnames<\/span> = <span class=\"code-snippet__built_in\">list<\/span>(gene,sample)))<\/span><\/code><code><span class=\"code-snippet_outer\">mat_0_1 <- as.data.frame(matrix(<span class=\"code-snippet__number\">0<\/span>,<span class=\"code-snippet__built_in\">length<\/span>(gene),<span class=\"code-snippet__built_in\">length<\/span>(sample),<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">dimnames<\/span> = <span class=\"code-snippet__built_in\">list<\/span>(gene,sample)))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (i <span class=\"code-snippet__keyword\">in<\/span> <span class=\"code-snippet__number\">1<\/span>:nrow(a)){<\/span><\/code><code><span class=\"code-snippet_outer\"> mat[<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">1<\/span>]),<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">3<\/span>])] <- <span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">2<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (i <span class=\"code-snippet__keyword\">in<\/span> <span class=\"code-snippet__number\">1<\/span>:nrow(a)){<\/span><\/code><code><span class=\"code-snippet_outer\"> mat_0_1[<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">1<\/span>]),<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">3<\/span>])] <- <span class=\"code-snippet__number\">1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6240\u6709\u6837\u672c\u7a81\u53d8\u60c5\u51b5\u6c47\u603b\/\u6392\u5e8f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene_count <- data.frame(gene=rownames(mat_0_1),<\/span><\/code><code><span class=\"code-snippet_outer\"> count=<span class=\"code-snippet__built_in\">as.numeric<\/span>(apply(mat_0_1,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__built_in\">sum<\/span>))) %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> arrange(desc(count))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5927\u5bb6\u53ef\u4ee5\u4fee\u6539\u6570\u5b5720\uff0c\u4ee3\u8868TOP\u591a\u5c11\uff0c\u4e5f\u53ef\u9009\u62e9\u81ea\u5df1\u611f\u5174\u8da3\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene_top <- gene_count$gene[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">20<\/span>] <span class=\"code-snippet__comment\">##\u4fdd\u5b58<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">save(mat,mat_0_1,file = <span class=\"code-snippet__string\">\"TMB.rda\"<\/span>) <span class=\"code-snippet__comment\">##\u4fdd\u5b58\u4e3aRData<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(mat,<span class=\"code-snippet__string\">\"all_mut_type.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(mat_0_1,<span class=\"code-snippet__string\">\"all_mut_01.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u770b\u4e00\u4e0b\u4fdd\u7559\u7684\u6570\u636e\u662f\u4ec0\u4e48\u6837\u5b50\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#all_mut_01.csv<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.34629629629629627\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/8_rVCKU4WS7S1D9hkluC3pC2FTicfw7A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1WjpE64cic3nvpLe7fhjvz0fCib2rVCKU4WS7S1D9hkluC3pC2FTicfw7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># all_mut_type.csv<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3472222222222222\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/9_bdE8fUkhLA5AN72oibnBg6MLA1M4lg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1pib2e6hGAmfFnC5Xh8Bcoy0ia8tibdE8fUkhLA5AN72oibnBg6MLA1M4lg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ec8\u4e8e\u83b7\u53d6\u5230\u60f3\u8981\u7684\u6570\u636e\u4e86\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u5f00\u59cb\u7ed8\u5236\u7011\u5e03\u56fe\u4e86<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">oncoplot(maf = all_mut,<\/span><\/code><code><span class=\"code-snippet_outer\">top = <span class=\"code-snippet__number\">20<\/span>, <span class=\"code-snippet__comment\">#\u663e\u793a\u524d20\u4e2a\u7684\u7a81\u53d8\u57fa\u56e0\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">fontSize = <span class=\"code-snippet__number\">0.6<\/span>, <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u5b57\u4f53\u5927\u5c0f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">showTumorSampleBarcodes = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#\u4e0d\u663e\u793a\u75c5\u4eba\u4fe1\u606f<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.4703703703703704\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_r36Z4kLSicIibabBFQyxaYU59JHX4w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1PqWEspiaSrdSVib3v5gjNemOoRKpr36Z4kLSicIibabBFQyxaYU59JHX4w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5927\u529f\u544a\u6210<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u8ba1\u7b97\u4e00\u4e0b\u6837\u672c\u7684TMB\u542b\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tmb_table = tmb(maf = all_mut) <span class=\"code-snippet__comment\">#\u9ed8\u8ba4\u4ee5log10\u8f6c\u5316\u7684TMB\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tmb_table = tmb(maf = all_mut,logScale = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#\u4e0dlog<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(tmb_table,<span class=\"code-snippet__string\">\"tmb_results.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f1a\u540c\u65f6\u7ed8\u5236\u4e00\u4e2a\u542b\u91cf\u56fe<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.10462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/11_UnY4xoDt5E1gbz8mxbiaE6LswD6rxw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1dp2iajC3mib7fyw0pxplh4A69wicUnY4xoDt5E1gbz8mxbiaE6LswD6rxw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u770b\u770b\u5bfc\u51fa\u7684\u8868\u683c<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.9462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/12_tXDh0TDRg05icPvy2ldCw5de8nzFJw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1NRWwn0TzCTx8wAJUSpwibUGicjptXDh0TDRg05icPvy2ldCw5de8nzFJw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u8fd9\u4e2a\u6570\u636e\u7684total_perMB\u5217\u5c31\u662f\u6211\u4eec\u9700\u8981\u7684TMB\u542b\u91cf<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;\">\n<section style=\"text-align: right;margin-right: 0%;margin-bottom: -20px;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);\"><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;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);\"><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 style=\"display: inline-block;vertical-align: top;width: auto;background-color: rgb(245, 241, 224);flex: 100 100 0%;align-self: flex-start;height: auto;border-right: 0px none rgb(62, 62, 62);border-top-right-radius: 12px;overflow: hidden;box-shadow: rgb(231, 215, 173) 0px 6px 0px;\">\n<section style=\"margin: 20px 0% 30px;\" powered-by=\"xiumi.us\">\n<section style=\"padding-right: 23px;padding-left: 23px;text-align: justify;font-size: 14px;line-height: 1.8;letter-spacing: 2px;\">\n<p>\u597d\u4e86\u670b\u53cb\u4eec\uff0c\u6570\u636e\u7684\u4e0b\u8f7d\u3001\u6574\u5408\u4ee5\u53ca\u57fa\u672c\u7ed8\u56fe\u5b8c\u6210\u4e86\uff0c\u8981\u77e5\u9053TMB\u5df2\u6210\u4e3a\u4e34\u5e8a\u4e0a\uff0c\u9884\u6d4b\u764c\u75c7\u514d\u75ab\u6cbb\u7597\u7597\u6548\u7684\u3001\u5177\u6709\u826f\u597d\u524d\u666f\u7684\u5168\u65b0\u751f\u7269\u6807\u5fd7\u7269\u3002\u65e2\u5f80\u7814\u7a76\u5df2\u7ecf\u8bc1\u5b9e\uff0c\u80bf\u7624\u7a81\u53d8\u8d1f\u8377\u9ad8\uff0c\u4e0e\u514d\u75ab\u6cbb\u7597\u7597\u6548\u5448\u6b63\u76f8\u5173\u3002\u6240\u4ee5\u6709\u4e86\u5206\u6790\u7ed3\u679c\u6240\u5f97\u7684TMB\u542b\u91cf\uff0c\u5c0f\u4f19\u4f34\u4eec\u77e5\u9053\u8be5\u5e72\u561b\u4e86\u5427\uff01<\/p>\n<p>\u6211\u4eec\u53ef\u4ee5\u5229\u7528\u8fd9\u4e2a\u6570\u636e\u53bb\u5c55\u5f00TMB\u751f\u5b58\u5206\u6790\u3001\u76f8\u5173\u6027\u5206\u6790\u7b49\u7b49\u4e00\u7cfb\u5217\u7684\u540e\u7eed\u5206\u6790\uff0c\u6216\u8bb8\u53ef\u4ee5\u4f7f\u5f97\u539f\u672c\u6734\u5b9e\u65e0\u534e\u7684\u8bba\u6587\u53d8\u5f97\u53d1\u5149\u53d1\u5f69\u54e6\uff01\u6bd5\u7adf\u8fd9\u5957\u6559\u7a0b\u53ef\u662f\u5927\u6d77\u54e5\u5455\u5fc3\u6ca5\u8840\u6574\u7406\u51fa\u6765\u7684\uff0c\u4f46\u662f\u5982\u679c\u80fd\u5bf9\u4f60\u6709\u5e2e\u52a9\uff0c\u90a3\u5c31\u503c\u5f97\uff0c\u5e0c\u671b\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u52a8\u624b\u8bd5\u4e00\u8bd5\uff01\u8bf4\u4e0d\u5b9a\u4f60\u80fd\u7528\u5f97\u4e0a\u5462\uff1f\uff08<strong><span style=\"color: rgb(59, 149, 115);\">\u6700\u540e\u63a8\u8350\u4e00\u4e0b\u5927\u6d77\u54e5\u65b0\u5f00\u53d1\u7684\u96f6\u4ee3\u7801\u4e91\u751f\u4fe1\u5206\u6790\u5de5\u5177\u5e73\u53f0\uff0c\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u4ef6\u51fa\u56fe\uff0c\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u6b22\u8fce\u6765\u53c2\u89c2\u54df\uff0c\u7f51\u5740\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/span><\/strong>\uff09<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\"><a target=\"_blank\" href=\"https:\/\/mp.weixin.qq.com\/s?__biz=MzAwNjE0MDY3MQ==&mid=2650761303&idx=2&sn=6f73471d1e82c56c0b2160d0fcd32d53&scene=21#wechat_redirect\" textvalue=\"\" linktype=\"image\" imgurl=\"https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/0?wx_fmt=jpeg\" imgdata=\"[object Object]\" 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3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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 style=\"display: inline-block;vertical-align: top;width: 50%;align-self: flex-start;flex: 0 0 auto;\">\n<section style=\"margin-top: 4px;margin-right: 0%;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 3px;height: 3px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 155px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 245, 245);\"><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>\n<\/section>\n<section style=\"text-align: center;transform: translate3d(3px, 0px, 0px);\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 0px;height: 0px;vertical-align: top;overflow: hidden;border-style: solid;border-width: 0px 0px 4px 4px;border-color: rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgba(255, 255, 255, 0) rgb(59, 149, 115);\"><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>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>\u5c0f\u4f19\u4f34\u4eec\u597d\u554a\uff0c\u6211\u662f\u5927\u6d77\u54e5\uff0c\u6700\u8fd1\u5927\u6d77\u54e5\u5728\u77e5\u8bc6\u7684\u6d77\u6d0b\u91cc\u6e38\u8361\u65f6\uff0c\u53d1\u73b0\u4e86\u5f88\u591aSCI\u6587\u7ae0\u4e2d\u90fd\u6709\u4e00\u79cd\u7528\u4e8e\u5c55\u793a\u80bf\u7624\u7ec6\u80de\u7a81\u53d8\u6570\u636e\u7684\u56fe\uff0c\u5927\u591a\u90fd\u662f\u4e0b\u56fe\u8fd9\u4e2a\u6a21\u6837\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.5990740740740741\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/1_YQzmicFGhWJ0zFCRAjD2X5ZkcdtzMw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1XnJZhSOtxjAFE9DYzcw9299t9YQzmicFGhWJ0zFCRAjD2X5ZkcdtzMw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\"><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u4e8e\u662f\u5927\u6d77\u54e5\u53c8\u53bb\u67e5\u9605\u5404\u7c7b\u76f8\u5173\u8bba\u6587\uff0c\u53d1\u73b0\u5927\u5bb6\u90fd\u79f0\u5176\u4e3a\u4f53\u7ec6\u80de\u7a81\u53d8\uff08somatic mutation\uff09\uff0c\u5176\u4e3b\u8981\u5c31\u662f\u5c55\u793a\u764c\u75c7\u4f53\u7ec6\u80de\u7684\u7a81\u53d8\u9891\u7387\uff0c\u540c\u65f6\u53ef\u4ee5\u6839\u636e\u8fd9\u4e2a\u6570\u636e\u8ba1\u7b97\u80bf\u7624\u7a81\u53d8\u8d1f\u8377\uff08Tumor Mutation Burden, TMB\uff09\uff0c\u800c\u8981\u60f3\u753b\u51fa\u8fd9\u5f20\u56fe\uff0c\u9996\u5148\u6211\u4eec\u5fc5\u987b\u8981\u51c6\u672c\u597d\u6570\u636e\u3002\u4eca\u5929\u5927\u6d77\u54e5\u5c31\u5148\u6765\u8ddf\u5927\u5bb6\u804a\u804a\u600e\u4e48\u4eceTCGA\u6570\u636e\u5e93\u4e0b\u8f7d\u4f53\u7ec6\u80de\u7a81\u53d8\u6570\u636e\u5e76\u8ba1\u7b97TMB\u503c\u3002<\/p>\n<p>\u9996\u5148\u6211\u4eec\u5148\u8fdb\u5165TCGA\u6570\u636e\u5e93\u4e3b\u9875\uff08https:\/\/portal.gdc.cancer.gov\/\uff09\u3002\u7136\u540e\u5c31\u53ef\u4ee5\u5728\u641c\u7d22\u6846\u4e2d\u8f93\u5165\u6211\u4eec\u611f\u5174\u8da3\u7684\u764c\u75c7ID\uff0c\u5982\u4e0b\u56fe\u6807\u8bb0\u6240\u793a\uff0c\u5927\u6d77\u54e5\u5c31\u7528\u5e38\u89c1\u7684\u80ba\u764c\u6570\u636e\u4e3a\u4f8b\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.45740740740740743\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/2_g009aMERR3nqSGcCAD8bdK1vsSiaXA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1rXWuDqKTJq2f9h7CUzCh0zN65g009aMERR3nqSGcCAD8bdK1vsSiaXA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u6211\u4eec\u70b9\u51fb\u4e0a\u9762\u7684\u68c0\u7d22\u63a8\u8350\u7b2c\u4e00\u4e2a\uff0c\u4f1a\u51fa\u73b0\u4e0b\u9762\u7684\u641c\u7d22\u7ed3\u679c\u9875\u9762\uff0c\u7136\u540e\u6211\u4eec\u70b9\u51fb\u56fe\u793a\u7684\u7ea2\u8272\u6807\u8bb0\u5904\u7684Simple Nucleotide Variation\u7684\u540e\u9762\u7684571\u4f8bcase\u5904<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.4564814814814815\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/3_xUpnVoWib95hYiaYM595K8KIAad8HA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1riciawu9wBhicVhYh35KlpY21iaRLsxUpnVoWib95hYiaYM595K8KIAad8HA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u70b9\u8fdb\u53bb\u540e\uff0c\u6211\u4eec\u53d1\u73b0\u6709\u7740\u5f88\u591a\u79cd\u7c7b\u7684\u6570\u636e\uff0c\u7136\u540e\u6211\u4eec\u9700\u8981\u4e00\u6b65\u4e00\u6b65\u7b5b\u9009\u51fa\u6211\u4eec\u9700\u8981\u7684\u7a81\u53d8\u6570\u636e\uff0c\u9700\u8981\u5927\u5bb6\u6309\u4e0b\u56fe\u6807\u8bb0\u52fe\u9009\uff0c\u5148\u70b9\u51fbFiles\uff0c\u52fe\u9009\u4e0asimple nucleotide variation\u3001Masked Somatic Mutation\u3001WXS\u3001maf\u3001open\u7b49\u9009\u9879\uff0c\u4e00\u4e2a\u90fd\u4e0d\u53ef\u4ee5\u6f0f\u54e6\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.4527777777777778\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/4_5PzA3HhfkzAibWQVqfAoIfAicibp0Q.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1tTph0mpXYaohnrS09jSx6QWxAy75PzA3HhfkzAibWQVqfAoIfAicibp0Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u5269\u4f59\u7684\u7ed3\u679c\u5c31\u662f\u6211\u4eec\u9700\u8981\u7684\u6570\u636e\uff0c\u63a5\u7740\u6211\u4eec\u9009\u62e9Case\uff0c\u70b9\u51fbAdd all Files to Cart\uff0c<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.4601851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_9TEdyYoxhziablxI2AMTmTWRasH5yw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1JFp0IBVmrLDomCGX4f7WgrpCS9TEdyYoxhziablxI2AMTmTWRasH5yw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u968f\u540e\u70b9\u51fb\u53f3\u4e0a\u89d2\u7684Cart\uff0c\u8fdb\u53bb\u540e\uff0c\u76f4\u63a5\u4e0b\u8f7d\uff0c\u9009\u62e9Cart\u5c31\u53ef\u4ee5\u5566\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3398148148148148\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/6_xLK7ibY9VpUiaYEazMFCAl0qATdruw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C11Cjn17FBib2nXM1pXxeCFxcSbcAxLK7ibY9VpUiaYEazMFCAl0qATdruw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a\u538b\u7f29\u5305\uff0c\u6211\u4eec\u9700\u8981\u628a\u5b83\u89e3\u538b\u653e\u5728\u6587\u4ef6\u5939\u4e2d\uff0c\u4f1a\u5f97\u5230\u5982\u56fe\u7684\u6587\u4ef6<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.7351851851851852\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_V6NG68fx8lvdLFzKXcNqIxwVBS7uag.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1Q6bWAsgpzUfkKTYibQwbVF2kLV6NG68fx8lvdLFzKXcNqIxwVBS7uag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u770b\u7740\u8fd9\u4e48\u591a\u6587\u4ef6\u5939\uff0c\u5f88\u591a\u5c0f\u4f19\u4f34\u80af\u5b9a\u61f5\u4e86\uff0c\u8fd9\u600e\u4e48\u5904\u7406\uff0c\u624b\u52a8\u6574\u5408\uff1f\u60f3\u60f3\u90fd\u5bb3\u6015\uff01\u522b\u62c5\u5fc3\uff0c\u5927\u6d77\u54e5\u6765\u5e2e\u4f60\uff0c\u7528\u4ee3\u7801\u4e00\u952e\u89e3\u51b3\uff01<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5148\u8bbe\u5b9a\u5de5\u4f5c\u76ee\u5f55\uff0c\u5c31\u8bbe\u7f6e\u4e3a\u89e3\u538b\u540e\u7684\u8def\u5f84<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">setwd(<span class=\"code-snippet__string\">\"C:\/Users\/Administrator\/Desktop\/gdc\/ gdc_download_20230809_022518.121743\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5bfc\u5165\u4e24\u4e2a\u5173\u952e\u7684R\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(maftools)<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u83b7\u53d6\u6240\u6709\u7684\u538b\u7f29\u6587\u4ef6\uff0c\u8fd9\u4e00\u6b65\u53ef\u80fd\u4f1a\u9700\u8981\u4e00\u4e9b\u65f6\u95f4\uff0c\u53d6\u51b3\u4e8e\u6211\u4eec\u7814\u7a76\u7684\u764c\u75c7\u6837\u672c\u89c4\u6a21\u5927\u5c0f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">files <- list.files(pattern = <span class=\"code-snippet__string\">'*.gz'<\/span>,recursive = <span class=\"code-snippet__literal\">TRUE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">all_mut <- data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (file <span class=\"code-snippet__keyword\">in<\/span> files) {<\/span><\/code><code><span class=\"code-snippet_outer\"> mut <- read.delim(file,skip = <span class=\"code-snippet__number\">7<\/span>, header = <span class=\"code-snippet__built_in\">T<\/span>, fill = <span class=\"code-snippet__literal\">TRUE<\/span>,sep = <span class=\"code-snippet__string\">\"t\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> all_mut <- rbind(all_mut,mut)<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6570\u636e\u6574\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">all_mut <- read.maf(all_mut)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">a <- all_mut@data %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> .[,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Hugo_Symbol\"<\/span>,<span class=\"code-snippet__string\">\"Variant_Classification\"<\/span>,<span class=\"code-snippet__string\">\"Tumor_Sample_Barcode\"<\/span>)] %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> as.data.frame() %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> mutate(Tumor_Sample_Barcode = substring(.$Tumor_Sample_Barcode,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">12<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">gene <- <span class=\"code-snippet__built_in\">as.character<\/span>(unique(a$Hugo_Symbol))<\/span><\/code><code><span class=\"code-snippet_outer\">sample <- <span class=\"code-snippet__built_in\">as.character<\/span>(unique(a$Tumor_Sample_Barcode))<\/span><\/code><code><span class=\"code-snippet_outer\">mat <- as.data.frame(matrix(<span class=\"code-snippet__string\">\"\"<\/span>,<span class=\"code-snippet__built_in\">length<\/span>(gene),<span class=\"code-snippet__built_in\">length<\/span>(sample),<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">dimnames<\/span> = <span class=\"code-snippet__built_in\">list<\/span>(gene,sample)))<\/span><\/code><code><span class=\"code-snippet_outer\">mat_0_1 <- as.data.frame(matrix(<span class=\"code-snippet__number\">0<\/span>,<span class=\"code-snippet__built_in\">length<\/span>(gene),<span class=\"code-snippet__built_in\">length<\/span>(sample),<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__built_in\">dimnames<\/span> = <span class=\"code-snippet__built_in\">list<\/span>(gene,sample)))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (i <span class=\"code-snippet__keyword\">in<\/span> <span class=\"code-snippet__number\">1<\/span>:nrow(a)){<\/span><\/code><code><span class=\"code-snippet_outer\"> mat[<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">1<\/span>]),<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">3<\/span>])] <- <span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">2<\/span>])<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (i <span class=\"code-snippet__keyword\">in<\/span> <span class=\"code-snippet__number\">1<\/span>:nrow(a)){<\/span><\/code><code><span class=\"code-snippet_outer\"> mat_0_1[<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">1<\/span>]),<span class=\"code-snippet__built_in\">as.character<\/span>(a[i,<span class=\"code-snippet__number\">3<\/span>])] <- <span class=\"code-snippet__number\">1<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6240\u6709\u6837\u672c\u7a81\u53d8\u60c5\u51b5\u6c47\u603b\/\u6392\u5e8f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene_count <- data.frame(gene=rownames(mat_0_1),<\/span><\/code><code><span class=\"code-snippet_outer\"> count=<span class=\"code-snippet__built_in\">as.numeric<\/span>(apply(mat_0_1,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__built_in\">sum<\/span>))) %>%<\/span><\/code><code><span class=\"code-snippet_outer\"> arrange(desc(count))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u5927\u5bb6\u53ef\u4ee5\u4fee\u6539\u6570\u5b5720\uff0c\u4ee3\u8868TOP\u591a\u5c11\uff0c\u4e5f\u53ef\u9009\u62e9\u81ea\u5df1\u611f\u5174\u8da3\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">gene_top <- gene_count$gene[<span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">20<\/span>] <span class=\"code-snippet__comment\">##\u4fdd\u5b58<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">save(mat,mat_0_1,file = <span class=\"code-snippet__string\">\"TMB.rda\"<\/span>) <span class=\"code-snippet__comment\">##\u4fdd\u5b58\u4e3aRData<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(mat,<span class=\"code-snippet__string\">\"all_mut_type.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(mat_0_1,<span class=\"code-snippet__string\">\"all_mut_01.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u770b\u4e00\u4e0b\u4fdd\u7559\u7684\u6570\u636e\u662f\u4ec0\u4e48\u6837\u5b50\u7684<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#all_mut_01.csv<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.34629629629629627\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/8_rVCKU4WS7S1D9hkluC3pC2FTicfw7A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1WjpE64cic3nvpLe7fhjvz0fCib2rVCKU4WS7S1D9hkluC3pC2FTicfw7A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># all_mut_type.csv<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.3472222222222222\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/9_bdE8fUkhLA5AN72oibnBg6MLA1M4lg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1pib2e6hGAmfFnC5Xh8Bcoy0ia8tibdE8fUkhLA5AN72oibnBg6MLA1M4lg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7ec8\u4e8e\u83b7\u53d6\u5230\u60f3\u8981\u7684\u6570\u636e\u4e86\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u5f00\u59cb\u7ed8\u5236\u7011\u5e03\u56fe\u4e86<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">oncoplot(maf = all_mut,<\/span><\/code><code><span class=\"code-snippet_outer\">top = <span class=\"code-snippet__number\">20<\/span>, <span class=\"code-snippet__comment\">#\u663e\u793a\u524d20\u4e2a\u7684\u7a81\u53d8\u57fa\u56e0\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">fontSize = <span class=\"code-snippet__number\">0.6<\/span>, <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u5b57\u4f53\u5927\u5c0f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">showTumorSampleBarcodes = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#\u4e0d\u663e\u793a\u75c5\u4eba\u4fe1\u606f<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.4703703703703704\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_r36Z4kLSicIibabBFQyxaYU59JHX4w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1PqWEspiaSrdSVib3v5gjNemOoRKpr36Z4kLSicIibabBFQyxaYU59JHX4w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u5927\u529f\u544a\u6210<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u6211\u4eec\u8ba1\u7b97\u4e00\u4e0b\u6837\u672c\u7684TMB\u542b\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tmb_table = tmb(maf = all_mut) <span class=\"code-snippet__comment\">#\u9ed8\u8ba4\u4ee5log10\u8f6c\u5316\u7684TMB\u7ed8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tmb_table = tmb(maf = all_mut,logScale = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#\u4e0dlog<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">write.csv(tmb_table,<span class=\"code-snippet__string\">\"tmb_results.csv\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4f1a\u540c\u65f6\u7ed8\u5236\u4e00\u4e2a\u542b\u91cf\u56fe<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" data-ratio=\"0.10462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/11_UnY4xoDt5E1gbz8mxbiaE6LswD6rxw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1dp2iajC3mib7fyw0pxplh4A69wicUnY4xoDt5E1gbz8mxbiaE6LswD6rxw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" class=\"rich_pages wxw-img\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u770b\u770b\u5bfc\u51fa\u7684\u8868\u683c<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"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=\"0.9462962962962963\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300dTCGA\u6570\u636e\u5e93maf\u7a81\u53d8\u6570\u636e\u5982\u4f55\u6574\u5408\u5e76\u7ed8\u5236\u7011\u5e03\u56fe\uff0c\u5927\u6d77\u54e5\u7ed9\u4f60\u7b54\u6848\/12_tXDh0TDRg05icPvy2ldCw5de8nzFJw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSTR3TgwvnmiaU9TehFsMX0C1NRWwn0TzCTx8wAJUSpwibUGicjptXDh0TDRg05icPvy2ldCw5de8nzFJw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"font-size: 14px;line-height: 1.8;letter-spacing: 2px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p>#\u8fd9\u4e2a\u6570\u636e\u7684total_perMB\u5217\u5c31\u662f\u6211\u4eec\u9700\u8981\u7684TMB\u542b\u91cf<\/p>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"display: flex;flex-flow: row;margin: 10px 0% 20px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: top;width: auto;flex: 0 0 0%;height: auto;align-self: flex-start;line-height: 0;\">\n<section style=\"text-align: right;margin-right: 0%;margin-bottom: -20px;margin-left: 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 8px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(245, 241, 224);\"><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;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 16px;height: 20px;vertical-align: top;overflow: hidden;border-width: 0px;border-radius: 21px 21px 0px 0px;border-style: none;border-color: rgb(62, 62, 62);background-color: rgb(231, 215, 173);\"><svg 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