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powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\">\u9996\u5148\uff0c\u6211\u4eec\u6765\u4e86\u89e3\u4e00\u4e0b\u62f7\u8d1d\u6570\u53d8\u5f02\u662f\u4ec0\u4e48\uff1f<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>\u62f7<\/strong><strong style=\"letter-spacing: 1.2px;\">\u8d1d\u6570\u53d8\u5f02\uff08Copy Number Variation\uff0cCNV\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u662f\u6307\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u7279\u5b9a\u57fa\u56e0\u6216\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u62f7\u8d1d\u6570\uff08\u590d\u5236\u6570\uff09\u5728\u4e0d\u540c\u4e2a\u4f53\u4e4b\u95f4\u53d1\u751f\u53d8\u5316\u7684\u73b0\u8c61\u3002\u6b63\u5e38\u60c5\u51b5\u4e0b\uff0c\u4eba\u7c7b\u6bcf\u4e2a\u7ec6\u80de\u90fd\u5e94\u8be5\u5305\u542b\u4e00\u4efd\u5b8c\u6574\u7684\u57fa\u56e0\u7ec4\uff0c\u5373\u6bcf\u4e2a\u57fa\u56e0\u6216\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u62f7\u8d1d\u6570\u4e3a2\uff08\u4e24\u4e2a\u7b49\u4f4d\u57fa\u56e0\uff0c\u4e00\u4e2a\u6765\u81ea\u6bcd\u4eb2\uff0c\u4e00\u4e2a\u6765\u81ea\u7236\u4eb2\uff09\u3002\u7136\u800c\uff0c\u7531\u4e8e\u57fa\u56e0\u7ec4\u590d\u5236\u548c\u7ef4\u62a4\u7684\u4e0d\u7a33\u5b9a\u6027\uff0c\u6709\u65f6\u5c31\u4f1a\u53d1\u751f\u62f7\u8d1d\u6570\u7684\u53d8\u5316\u3002\u5e76\u4e14\u5b83\u4eec\u53ef\u80fd\u5bf9\u4e2a\u4f53\u7684\u8868\u578b\u7279\u5f81\u3001\u75be\u75c5\u6613\u611f\u6027\u4ee5\u53ca\u836f\u7269\u53cd\u5e94\u7b49\u4ea7\u751f\u5f71\u54cd<\/p>\n<p>\u4e86\u89e3\u4e86CNV\u662f\u4ec0\u4e48\uff0c\u90a3\u6211\u4eec\u5c31\u5f00\u59cb\u6765\u4e86\u89e3\u4e00\u4e0b\u5982\u4f55\u5904\u7406CNV\u6570\u636e\u5427\u3002<\/p>\n<p>\u9996\u5148\u6211\u4eec\u8981\u4eceTCGA\u4e2d\u4e0b\u8f7d\u5bf9\u5e94\u7684CNV\u6570\u636e\uff0c\u4e00\u5171\u6709\u4e24\u79cd\uff0c\u5206\u522b\u4e3aCopy Number Segment\u548cMasked Copy Number Segment\uff0c\u6211\u4eec\u770b\u770b\u5b98\u65b9\u89e3\u91ca\uff1a<\/p>\n<p>Copy Number Segment\uff1a\u5c06\u8fde\u7eed\u67d3\u8272\u4f53\u7247\u6bb5\u4e0e\u57fa\u56e0\u7ec4\u5750\u6807\u3001\u5e73\u5747\u9635\u5217\u5f3a\u5ea6\u4ee5\u53ca\u4e0e\u6bcf\u4e2a\u7247\u6bb5\u7ed3\u5408\u7684\u63a2\u9488\u6570\u91cf\u76f8\u5173\u8054\u7684\u8868\u683c\u3002<\/p>\n<p>Masked Copy Number Segment\uff1a\u5220\u9664\u4e86\u5e26\u6709\u5df2\u77e5\u542b\u6709\u79cd\u7cfb\u7a81\u53d8\u7684\u63a2\u9488\u7684\u7247\u6bb5\uff0c\u4e14\u4e0e\u62f7\u8d1d\u6570\u7247\u6bb5\u5177\u6709\u76f8\u540c\u4fe1\u606f\u7684\u8868<\/p>\n<p>\u7136\u540e\u6211\u4eec\u672c\u6b21\u5206\u6790\u9009\u62e9Masked Copy Number Segment \u6570\u636e\uff0c\u662f\u4e00\u4e2agz\u683c\u5f0f\u7684\u538b\u7f29\u5305\uff0c\u6211\u4eec\u89e3\u538b\u540e\u8fdb\u884c\u5904\u7406\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4e0a\u4ee3\u7801\uff01<\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">rm(<span class=\"code-snippet__built_in\">list<\/span> = ls())<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06\u6574\u7406\u597d\u7684Masked Copy Number Segment\u91cd\u65b0\u547d\u540d\u4e3a\u201crawdata\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(dir(<span class=\"code-snippet__string\">\"rawdata\"<\/span>) )<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u521b\u5efa\u4e00\u4e2a\u7528\u6765\u653etxt\u6587\u4ef6\u7684\u6587\u4ef6\u5939\uff0c\u56e0\u4e3a\u89e3\u538b\u540e\u8fd8\u6709\u591a\u4e2a\u538b\u7f29\u5305\uff0c\u6bcf\u4e2a\u538b\u7f29\u5305\u5305\u542b\u4e00\u4e2atxt\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dir.create(<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7528lapply\u5c06rawdata\u91cc\u9762txt\u6587\u4ef6\u6574\u7406\u5230\u4e00\u4e2a\u6587\u4ef6\u5939\u91cc<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> raw_txt <- dir(<span class=\"code-snippet__string\">\"rawdata\/\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">lapply(raw_txt, <span class=\"code-snippet__keyword\">function<\/span>(x){<\/span><\/code><code><span class=\"code-snippet_outer\"> mydir <- paste0(<span class=\"code-snippet__string\">\".\/rawdata\/\"<\/span>,x)<\/span><\/code><code><span class=\"code-snippet_outer\"> file <- list.files(mydir,pattern = <span class=\"code-snippet__string\">\"nocnv_grch38\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> myfile <- paste0(<span class=\"code-snippet__string\">\".\/rawdata\/\"<\/span>,x,<span class=\"code-snippet__string\">\"\/\"<\/span>,file)<\/span><\/code><code><span class=\"code-snippet_outer\"> file.copy(myfile,<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\">})<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\">\u6700\u540e\u4f1a\u5f97\u5230\u591a\u4e2atxt\u6587\u4ef6\uff0c\u5982\u4e0b\u56fe<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.1098591549295775\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_cpveJDEVSyCdGPVUibeUEHPn2ch4FA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra7IX9hAqmEqSZUKH0wmk5b3kSAcpveJDEVSyCdGPVUibeUEHPn2ch4FA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"355\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5f00\u59cb\u6574\u5408\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(data.table)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_file <- dir(<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_file[<span class=\"code-snippet__number\">1<\/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=\"0.08396946564885496\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qOX2PyGUFzKm17wQtyibmhwNxDtZaA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrracwcSIIuPwmsSt4M9ViagJePauaqOX2PyGUFzKm17wQtyibmhwNxDtZaA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"393\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">file <- paste0(<span class=\"code-snippet__string\">\".\/rawdata_all\/\"<\/span>,cnv_file<\/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=\"0.22244897959183674\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_tibJc19YAYA57pdF2ibibLBYu0ABgg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraQadwO6Sw1j8EB7Gwp2z0wmz9fQwtibJc19YAYA57pdF2ibibLBYu0ABgg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"490\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u6279\u91cf\u8bfb\u53d6txt\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">file_list <- <span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">fred_cnv <- <span class=\"code-snippet__keyword\">function<\/span>(x){<\/span><\/code><code><span class=\"code-snippet_outer\"> file_list[[x]] <- data.table::fread(file = x,data.table = <span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> file_list[[x]] <\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- lapply(file, fred_cnv)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u884c\u5408\u5e76<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- do.call(bind_row,cnv_df)<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.37169517884914466\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_iappxLicaYrB7XWBAe5J29l5mDeFBw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraDIlico2ibeFMD7R50QpiaXHApEjKeiappxLicaYrB7XWBAe5J29l5mDeFBw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"643\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u8bfb\u53d6metadata\u91cc\u9762\u7684\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- jsonlite::fromJSON(<span class=\"code-snippet__string\">\"metadata.cart.2021-02-15.json\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata_id <- metadata %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> dplyr::select(<span class=\"code-snippet__built_in\">c<\/span>(file_name,associated_entities)) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">meta_df <- do.call(rbind,metadata$associated_entities)<\/span><\/code><code><span class=\"code-snippet_outer\">head(metadata_id,<span class=\"code-snippet__number\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1743827160493827\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_714qoazrT26oNbN56p70a9wDibiboQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrrajwtLPzWVPYFBnhTNh4MZQ6hZbX714qoazrT26oNbN56p70a9wDibiboQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"648\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">cnv_df$Sample <- meta_df$entity_submitter_id[match(cnv_df$GDC_Aliquot,meta_df$entity_id)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(unique(cnv_df$GDC_Aliquot))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 1025<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(unique(cnv_df$Sample))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 1025<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3689922480620155\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_N2lMIrDRiabax2icYae7x02l2PI69g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrrah1MrSLTaldcAibiaUbjc052UQLEVN2lMIrDRiabax2icYae7x02l2PI69g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"645\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u628a\u6837\u672c\u540d\u6539\u4e00\u4e0b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df$Sample <- substring(cnv_df$Sample,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">16<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.369969040247678\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_yZFSIAxyOvTYh6CFURRnrbCDlXqSSg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraqHw8nLueVZWYY4ibPibpDwIcEqyZFSIAxyOvTYh6CFURRnrbCDlXqSSg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"646\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## Gistic2.0\u53ea\u9700\u8981maskedCNS\u7684\u516d\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- cnv_df[,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">'Sample'<\/span>,<span class=\"code-snippet__string\">'Chromosome'<\/span>,<span class=\"code-snippet__string\">'Start'<\/span>,<span class=\"code-snippet__string\">'End'<\/span>,<span class=\"code-snippet__string\">'Num_Probes'<\/span>,<span class=\"code-snippet__string\">'Segment_Mean'<\/span>)]<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.20706260032102727\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_e7gfbcPDiaR1fANf3AN80qtSRZ2eGw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraANjBPaKuJVUCMDPATRuiaLApOqe7gfbcPDiaR1fANf3AN80qtSRZ2eGw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"623\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u597d\u4e86\uff0c\u6574\u7406\u5b8c\u6bd5\uff0c\u73b0\u5728\u8fd9\u4e2a\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u62ff\u53bb\u5206\u6790\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u522b\u7740\u6025\uff01\u8fd8\u6709\u4e00\u4e2a\u6570\u636e\u9700\u8981\u6574\u7406\u5462\uff01\u56e0\u4e3aGISTIC2.0\u9700\u8981\u4e24\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u6211\u4eec\u4e4b\u6574\u7406\u4e86\u4e00\u4e2a\uff0c\u8fd8\u6709\u4e00\u4e2amarker file\u6570\u636e\u9700\u8981\u6574\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9700\u8981\u5728https:\/\/gdc.cancer.gov\/about-data\/gdc-data-processing\/gdc-reference-files\u4e2d\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u7684\u201cSNP6 GRCh38 Remapped Probeset File for Copy Number Variation Analysis\u201d\u6587\u4ef6\uff0c\u540d\u5b57\u4e3asnp6.na35.remap.hg38.subset.txt.gz\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0b\u8f7d\u540e\uff0c\u5f00\u59cb\u4ee3\u7801\u5904\u7406\u90e8\u5206\u5427<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">hg38_marker_file <- read.delim(<span class=\"code-snippet__string\">\"snp6.na35.remap.hg38.subset.txt.gz\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(hg38_marker_file )<\/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=\"0.2535211267605634\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_m1siaK60rAoibpW1w3kxukiaao4nWQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra32yg9O4Dh1PDNX2ILVibuzNYOvbpm1siaK60rAoibpW1w3kxukiaao4nWQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"497\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6839\u636e\u5b98\u65b9\u63d0\u793aIf you are using Masked Copy Number Segment for GISTIC analysis, please only keep probesets with freqcnv = FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u53ea\u7528\u4fdd\u7559freqcnv = FALSE\u7684\u6570\u636e\u5c31\u597d\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">hg_marker_file <- hg38_marker_file[hg38_marker_file$freqcnv==<span class=\"code-snippet__string\">\"FALSE\"<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\">hg_marker_file <- hg_marker_file [,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">2<\/span>,<span class=\"code-snippet__number\">3<\/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=\"0.4558303886925795\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_087zabK9asVfRE1NNJacTkTBqt9YvA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra0y59pj1zcfkejRHCfTD1m9H3087zabK9asVfRE1NNJacTkTBqt9YvA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"283\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u5c31\u597d\u5566\uff0c\u53ea\u7528\u8fd9\u4e09\u5217\u5c31\u53ef\u4ee5\u4e86\u3002<\/p>\n<p>\u73b0\u5728\u6211\u4eec\u5c31\u83b7\u5f97\u4e86\u4e24\u4e2a\u6570\u636e\uff0c\u4e00\u4e2aCNV\u6570\u636e\u548c\u4e00\u4e2amarker file\u6570\u636e\uff0c\u53ea\u9700\u8fd9\u4e24\u4e2a\u6587\u4ef6\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528GISTIC2.0\u5c55\u5f00\u5206\u6790\u5566\u3002<\/p>\n<\/section>\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: 10px;padding-left: 10px;text-align: justify;\">\n<p>\u597d\u4e86\uff0c\u672c\u6b21\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff01\u603b\u7ed3\u4e00\u4e0b\uff01GISTIC2.0\u5bf9\u4e8e\u6570\u636e\u7684\u8981\u6c42\u8fd8\u662f\u6bd4\u8f83\u82db\u523b\u7684\uff0c\u5f88\u591a\u5c0f\u4f19\u4f34\u8fd9\u4e00\u6b65\u7684\u5931\u8bef\u5c31\u5bfc\u81f4\u4e86\u540e\u7eed\u5206\u6790\u65e0\u6cd5\u8fdb\u884c\uff0c\u6240\u4ee5\u5927\u5bb6\u4e00\u5b9a\u8981\u597d\u597d\u6ce8\u610f\u5927\u6d77\u54e5\u7684\u4ee3\u7801\u7ec6\u8282\uff0c\u4e0d\u8981\u7c97\u5fc3\u5927\u610f\u54e6\uff01<\/p>\n<p>\u4e0b\u4e00\u6b21\u5927\u6d77\u54e5\u4f1a\u5206\u4eab\u5982\u4f55\u7528\u672c\u6b21\u6574\u7406\u597d\u7684\u6587\u4ef6\u4f7f\u7528GISTIC2.0\u5728\u7ebf\u5206\u6790\u6765\u5f97\u5230Amplification GISTIC plot \u4ee5\u53caDeletion GISTIC plot\u4e24\u5f20\u5173\u952e\u56fe\uff0c\u540c\u65f6\u5229\u7528maftools\u6765\u53ef\u89c6\u5316\u7ed3\u679c\u6587\u4ef6\u4ee5\u53ca\u6311\u9009\u62f7\u8d1d\u6570\u5dee\u5f02\u57fa\u56e0\u54e6\uff01\u5927\u5bb6\u4e0d\u8981\u9519\u8fc7\u54e6\uff01\uff08\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\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\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\uff09<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 12px;\" powered-by=\"xiumi.us\">\n<p><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]\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.35083798882681566\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_ocafb5YBQcZWdQRrtP2Xo7vaFWaecA.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"895\" style=\"\" data-recalc-dims=\"1\" \/><\/span><\/a><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_07T3ukOr5mxE6sbTMZvYNklUgT3oKg.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYQlIrRTwqxXypnzYht7bhh3T07T3ukOr5mxE6sbTMZvYNklUgT3oKg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u70b9\u51fb\u201c\u9605\u8bfb\u539f\u6587\u201d\u8fdb\u5165\u7f51\u5740<\/p>\n<\/section>\n<section style=\"margin-left: 8%;margin-right: 8%;line-height: 1.1em;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;vertical-align: top;border-top: 1em solid rgb(0, 150, 136);border-left: 0.8em solid transparent !important;border-right: 0.8em solid transparent !important;\"><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 style=\"font-size: 11px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e0d\u53ef\u591a\u5f97\u7684GISTIC2.0\u6559\u5b66\u4e4bTCGA\u62f7\u8d1d\u6570\u53d8\u5f02CNV\u6570\u636e\u6574\u7406 \u5927\u6d77\u54e5 \u751f\u4fe1\u679c&nb […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=58764"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764\/revisions"}],"predecessor-version":[{"id":58777,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764\/revisions\/58777"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58764"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58764"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58764"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":58764,"date":"2024-06-16T23:34:57","date_gmt":"2024-06-16T15:34:57","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58764"},"modified":"2024-06-16T23:34:57","modified_gmt":"2024-06-16T15:34:57","slug":"%e4%b8%8d%e5%8f%af%e5%a4%9a%e5%be%97%e7%9a%84gistic2-0%e6%95%99%e5%ad%a6%e4%b9%8btcga%e6%8b%b7%e8%b4%9d%e6%95%b0%e5%8f%98%e5%bc%82cnv%e6%95%b0%e6%8d%ae%e6%95%b4%e7%90%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=58764","title":{"rendered":"\u4e0d\u53ef\u591a\u5f97\u7684GISTIC2.0\u6559\u5b66\u4e4bTCGA\u62f7\u8d1d\u6570\u53d8\u5f02CNV\u6570\u636e\u6574\u7406"},"content":{"rendered":"

\n
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powered-by=\"xiumi.us\"><br \/><\/p>\n<p powered-by=\"xiumi.us\">\u9996\u5148\uff0c\u6211\u4eec\u6765\u4e86\u89e3\u4e00\u4e0b\u62f7\u8d1d\u6570\u53d8\u5f02\u662f\u4ec0\u4e48\uff1f<\/p>\n<section style=\"text-align: left;justify-content: flex-start;margin-top: 20px;margin-bottom: 10px;display: flex;flex-flow: row;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;background-color: rgb(59, 149, 115);min-width: 10%;flex: 0 0 auto;height: auto;align-self: flex-start;\">\n<section style=\"color: rgb(245, 245, 245);text-align: center;letter-spacing: 1px;padding-right: 10px;padding-left: 10px;\" powered-by=\"xiumi.us\">\n<p><strong>\u62f7<\/strong><strong style=\"letter-spacing: 1.2px;\">\u8d1d\u6570\u53d8\u5f02\uff08Copy Number Variation\uff0cCNV\uff09<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u662f\u6307\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u7279\u5b9a\u57fa\u56e0\u6216\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u62f7\u8d1d\u6570\uff08\u590d\u5236\u6570\uff09\u5728\u4e0d\u540c\u4e2a\u4f53\u4e4b\u95f4\u53d1\u751f\u53d8\u5316\u7684\u73b0\u8c61\u3002\u6b63\u5e38\u60c5\u51b5\u4e0b\uff0c\u4eba\u7c7b\u6bcf\u4e2a\u7ec6\u80de\u90fd\u5e94\u8be5\u5305\u542b\u4e00\u4efd\u5b8c\u6574\u7684\u57fa\u56e0\u7ec4\uff0c\u5373\u6bcf\u4e2a\u57fa\u56e0\u6216\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u62f7\u8d1d\u6570\u4e3a2\uff08\u4e24\u4e2a\u7b49\u4f4d\u57fa\u56e0\uff0c\u4e00\u4e2a\u6765\u81ea\u6bcd\u4eb2\uff0c\u4e00\u4e2a\u6765\u81ea\u7236\u4eb2\uff09\u3002\u7136\u800c\uff0c\u7531\u4e8e\u57fa\u56e0\u7ec4\u590d\u5236\u548c\u7ef4\u62a4\u7684\u4e0d\u7a33\u5b9a\u6027\uff0c\u6709\u65f6\u5c31\u4f1a\u53d1\u751f\u62f7\u8d1d\u6570\u7684\u53d8\u5316\u3002\u5e76\u4e14\u5b83\u4eec\u53ef\u80fd\u5bf9\u4e2a\u4f53\u7684\u8868\u578b\u7279\u5f81\u3001\u75be\u75c5\u6613\u611f\u6027\u4ee5\u53ca\u836f\u7269\u53cd\u5e94\u7b49\u4ea7\u751f\u5f71\u54cd<\/p>\n<p>\u4e86\u89e3\u4e86CNV\u662f\u4ec0\u4e48\uff0c\u90a3\u6211\u4eec\u5c31\u5f00\u59cb\u6765\u4e86\u89e3\u4e00\u4e0b\u5982\u4f55\u5904\u7406CNV\u6570\u636e\u5427\u3002<\/p>\n<p>\u9996\u5148\u6211\u4eec\u8981\u4eceTCGA\u4e2d\u4e0b\u8f7d\u5bf9\u5e94\u7684CNV\u6570\u636e\uff0c\u4e00\u5171\u6709\u4e24\u79cd\uff0c\u5206\u522b\u4e3aCopy Number Segment\u548cMasked Copy Number Segment\uff0c\u6211\u4eec\u770b\u770b\u5b98\u65b9\u89e3\u91ca\uff1a<\/p>\n<p>Copy Number Segment\uff1a\u5c06\u8fde\u7eed\u67d3\u8272\u4f53\u7247\u6bb5\u4e0e\u57fa\u56e0\u7ec4\u5750\u6807\u3001\u5e73\u5747\u9635\u5217\u5f3a\u5ea6\u4ee5\u53ca\u4e0e\u6bcf\u4e2a\u7247\u6bb5\u7ed3\u5408\u7684\u63a2\u9488\u6570\u91cf\u76f8\u5173\u8054\u7684\u8868\u683c\u3002<\/p>\n<p>Masked Copy Number Segment\uff1a\u5220\u9664\u4e86\u5e26\u6709\u5df2\u77e5\u542b\u6709\u79cd\u7cfb\u7a81\u53d8\u7684\u63a2\u9488\u7684\u7247\u6bb5\uff0c\u4e14\u4e0e\u62f7\u8d1d\u6570\u7247\u6bb5\u5177\u6709\u76f8\u540c\u4fe1\u606f\u7684\u8868<\/p>\n<p>\u7136\u540e\u6211\u4eec\u672c\u6b21\u5206\u6790\u9009\u62e9Masked Copy Number Segment \u6570\u636e\uff0c\u662f\u4e00\u4e2agz\u683c\u5f0f\u7684\u538b\u7f29\u5305\uff0c\u6211\u4eec\u89e3\u538b\u540e\u8fdb\u884c\u5904\u7406\u3002<\/p>\n<\/section>\n<section style=\"font-size: 12px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<p powered-by=\"xiumi.us\">\u4e0a\u4ee3\u7801\uff01<\/p>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">rm(<span class=\"code-snippet__built_in\">list<\/span> = ls())<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u5c06\u6574\u7406\u597d\u7684Masked Copy Number Segment\u91cd\u65b0\u547d\u540d\u4e3a\u201crawdata\u201d<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(dir(<span class=\"code-snippet__string\">\"rawdata\"<\/span>) )<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u521b\u5efa\u4e00\u4e2a\u7528\u6765\u653etxt\u6587\u4ef6\u7684\u6587\u4ef6\u5939\uff0c\u56e0\u4e3a\u89e3\u538b\u540e\u8fd8\u6709\u591a\u4e2a\u538b\u7f29\u5305\uff0c\u6bcf\u4e2a\u538b\u7f29\u5305\u5305\u542b\u4e00\u4e2atxt\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dir.create(<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7528lapply\u5c06rawdata\u91cc\u9762txt\u6587\u4ef6\u6574\u7406\u5230\u4e00\u4e2a\u6587\u4ef6\u5939\u91cc<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> raw_txt <- dir(<span class=\"code-snippet__string\">\"rawdata\/\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">lapply(raw_txt, <span class=\"code-snippet__keyword\">function<\/span>(x){<\/span><\/code><code><span class=\"code-snippet_outer\"> mydir <- paste0(<span class=\"code-snippet__string\">\".\/rawdata\/\"<\/span>,x)<\/span><\/code><code><span class=\"code-snippet_outer\"> file <- list.files(mydir,pattern = <span class=\"code-snippet__string\">\"nocnv_grch38\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> myfile <- paste0(<span class=\"code-snippet__string\">\".\/rawdata\/\"<\/span>,x,<span class=\"code-snippet__string\">\"\/\"<\/span>,file)<\/span><\/code><code><span class=\"code-snippet_outer\"> file.copy(myfile,<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\">})<\/span><\/code><\/pre>\n<\/section>\n<p powered-by=\"xiumi.us\">\u6700\u540e\u4f1a\u5f97\u5230\u591a\u4e2atxt\u6587\u4ef6\uff0c\u5982\u4e0b\u56fe<\/p>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.1098591549295775\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_cpveJDEVSyCdGPVUibeUEHPn2ch4FA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra7IX9hAqmEqSZUKH0wmk5b3kSAcpveJDEVSyCdGPVUibeUEHPn2ch4FA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"355\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u7136\u540e\u5f00\u59cb\u6574\u5408\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(data.table)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_file <- dir(<span class=\"code-snippet__string\">\"rawdata_all\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_file[<span class=\"code-snippet__number\">1<\/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=\"0.08396946564885496\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_qOX2PyGUFzKm17wQtyibmhwNxDtZaA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrracwcSIIuPwmsSt4M9ViagJePauaqOX2PyGUFzKm17wQtyibmhwNxDtZaA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"393\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">file <- paste0(<span class=\"code-snippet__string\">\".\/rawdata_all\/\"<\/span>,cnv_file<\/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=\"0.22244897959183674\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_tibJc19YAYA57pdF2ibibLBYu0ABgg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraQadwO6Sw1j8EB7Gwp2z0wmz9fQwtibJc19YAYA57pdF2ibibLBYu0ABgg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"490\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u6279\u91cf\u8bfb\u53d6txt\u6587\u4ef6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">file_list <- <span class=\"code-snippet__built_in\">list<\/span>()<\/span><\/code><code><span class=\"code-snippet_outer\">fred_cnv <- <span class=\"code-snippet__keyword\">function<\/span>(x){<\/span><\/code><code><span class=\"code-snippet_outer\"> file_list[[x]] <- data.table::fread(file = x,data.table = <span class=\"code-snippet__built_in\">F<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> file_list[[x]] <\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- lapply(file, fred_cnv)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u884c\u5408\u5e76<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- do.call(bind_row,cnv_df)<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.37169517884914466\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_iappxLicaYrB7XWBAe5J29l5mDeFBw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraDIlico2ibeFMD7R50QpiaXHApEjKeiappxLicaYrB7XWBAe5J29l5mDeFBw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"643\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u8bfb\u53d6metadata\u91cc\u9762\u7684\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- jsonlite::fromJSON(<span class=\"code-snippet__string\">\"metadata.cart.2021-02-15.json\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata_id <- metadata %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> dplyr::select(<span class=\"code-snippet__built_in\">c<\/span>(file_name,associated_entities)) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">meta_df <- do.call(rbind,metadata$associated_entities)<\/span><\/code><code><span class=\"code-snippet_outer\">head(metadata_id,<span class=\"code-snippet__number\">2<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.1743827160493827\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_714qoazrT26oNbN56p70a9wDibiboQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrrajwtLPzWVPYFBnhTNh4MZQ6hZbX714qoazrT26oNbN56p70a9wDibiboQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"648\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">cnv_df$Sample <- meta_df$entity_submitter_id[match(cnv_df$GDC_Aliquot,meta_df$entity_id)]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(unique(cnv_df$GDC_Aliquot))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 1025<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">length<\/span>(unique(cnv_df$Sample))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## [1] 1025<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.3689922480620155\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_N2lMIrDRiabax2icYae7x02l2PI69g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrrah1MrSLTaldcAibiaUbjc052UQLEVN2lMIrDRiabax2icYae7x02l2PI69g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"645\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u628a\u6837\u672c\u540d\u6539\u4e00\u4e0b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df$Sample <- substring(cnv_df$Sample,<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">16<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.369969040247678\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_yZFSIAxyOvTYh6CFURRnrbCDlXqSSg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraqHw8nLueVZWYY4ibPibpDwIcEqyZFSIAxyOvTYh6CFURRnrbCDlXqSSg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"646\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## Gistic2.0\u53ea\u9700\u8981maskedCNS\u7684\u516d\u5217<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">cnv_df <- cnv_df[,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">'Sample'<\/span>,<span class=\"code-snippet__string\">'Chromosome'<\/span>,<span class=\"code-snippet__string\">'Start'<\/span>,<span class=\"code-snippet__string\">'End'<\/span>,<span class=\"code-snippet__string\">'Num_Probes'<\/span>,<span class=\"code-snippet__string\">'Segment_Mean'<\/span>)]<\/span><\/code><code><span class=\"code-snippet_outer\">head(cnv_df)<\/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=\"0.20706260032102727\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_e7gfbcPDiaR1fANf3AN80qtSRZ2eGw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrraANjBPaKuJVUCMDPATRuiaLApOqe7gfbcPDiaR1fANf3AN80qtSRZ2eGw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"623\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u597d\u4e86\uff0c\u6574\u7406\u5b8c\u6bd5\uff0c\u73b0\u5728\u8fd9\u4e2a\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u62ff\u53bb\u5206\u6790\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u522b\u7740\u6025\uff01\u8fd8\u6709\u4e00\u4e2a\u6570\u636e\u9700\u8981\u6574\u7406\u5462\uff01\u56e0\u4e3aGISTIC2.0\u9700\u8981\u4e24\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u6211\u4eec\u4e4b\u6574\u7406\u4e86\u4e00\u4e2a\uff0c\u8fd8\u6709\u4e00\u4e2amarker file\u6570\u636e\u9700\u8981\u6574\u7406<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u9700\u8981\u5728https:\/\/gdc.cancer.gov\/about-data\/gdc-data-processing\/gdc-reference-files\u4e2d\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u7684\u201cSNP6 GRCh38 Remapped Probeset File for Copy Number Variation Analysis\u201d\u6587\u4ef6\uff0c\u540d\u5b57\u4e3asnp6.na35.remap.hg38.subset.txt.gz\u3002<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u4e0b\u8f7d\u540e\uff0c\u5f00\u59cb\u4ee3\u7801\u5904\u7406\u90e8\u5206\u5427<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">hg38_marker_file <- read.delim(<span class=\"code-snippet__string\">\"snp6.na35.remap.hg38.subset.txt.gz\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">head(hg38_marker_file )<\/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=\"0.2535211267605634\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_m1siaK60rAoibpW1w3kxukiaao4nWQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra32yg9O4Dh1PDNX2ILVibuzNYOvbpm1siaK60rAoibpW1w3kxukiaao4nWQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"497\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6839\u636e\u5b98\u65b9\u63d0\u793aIf you are using Masked Copy Number Segment for GISTIC analysis, please only keep probesets with freqcnv = FALSE<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#\u6211\u4eec\u53ea\u7528\u4fdd\u7559freqcnv = FALSE\u7684\u6570\u636e\u5c31\u597d\u5566\uff01<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">hg_marker_file <- hg38_marker_file[hg38_marker_file$freqcnv==<span class=\"code-snippet__string\">\"FALSE\"<\/span>,]<\/span><\/code><code><span class=\"code-snippet_outer\">hg_marker_file <- hg_marker_file [,<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">1<\/span>,<span class=\"code-snippet__number\">2<\/span>,<span class=\"code-snippet__number\">3<\/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=\"0.4558303886925795\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_087zabK9asVfRE1NNJacTkTBqt9YvA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/YHGRXkSxjSSM3zOUx6mYaHf3ENhpwrra0y59pj1zcfkejRHCfTD1m9H3087zabK9asVfRE1NNJacTkTBqt9YvA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"283\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u5c31\u597d\u5566\uff0c\u53ea\u7528\u8fd9\u4e09\u5217\u5c31\u53ef\u4ee5\u4e86\u3002<\/p>\n<p>\u73b0\u5728\u6211\u4eec\u5c31\u83b7\u5f97\u4e86\u4e24\u4e2a\u6570\u636e\uff0c\u4e00\u4e2aCNV\u6570\u636e\u548c\u4e00\u4e2amarker file\u6570\u636e\uff0c\u53ea\u9700\u8fd9\u4e24\u4e2a\u6587\u4ef6\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528GISTIC2.0\u5c55\u5f00\u5206\u6790\u5566\u3002<\/p>\n<\/section>\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: 10px;padding-left: 10px;text-align: justify;\">\n<p>\u597d\u4e86\uff0c\u672c\u6b21\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff01\u603b\u7ed3\u4e00\u4e0b\uff01GISTIC2.0\u5bf9\u4e8e\u6570\u636e\u7684\u8981\u6c42\u8fd8\u662f\u6bd4\u8f83\u82db\u523b\u7684\uff0c\u5f88\u591a\u5c0f\u4f19\u4f34\u8fd9\u4e00\u6b65\u7684\u5931\u8bef\u5c31\u5bfc\u81f4\u4e86\u540e\u7eed\u5206\u6790\u65e0\u6cd5\u8fdb\u884c\uff0c\u6240\u4ee5\u5927\u5bb6\u4e00\u5b9a\u8981\u597d\u597d\u6ce8\u610f\u5927\u6d77\u54e5\u7684\u4ee3\u7801\u7ec6\u8282\uff0c\u4e0d\u8981\u7c97\u5fc3\u5927\u610f\u54e6\uff01<\/p>\n<p>\u4e0b\u4e00\u6b21\u5927\u6d77\u54e5\u4f1a\u5206\u4eab\u5982\u4f55\u7528\u672c\u6b21\u6574\u7406\u597d\u7684\u6587\u4ef6\u4f7f\u7528GISTIC2.0\u5728\u7ebf\u5206\u6790\u6765\u5f97\u5230Amplification GISTIC plot \u4ee5\u53caDeletion GISTIC plot\u4e24\u5f20\u5173\u952e\u56fe\uff0c\u540c\u65f6\u5229\u7528maftools\u6765\u53ef\u89c6\u5316\u7ed3\u679c\u6587\u4ef6\u4ee5\u53ca\u6311\u9009\u62f7\u8d1d\u6570\u5dee\u5f02\u57fa\u56e0\u54e6\uff01\u5927\u5bb6\u4e0d\u8981\u9519\u8fc7\u54e6\uff01\uff08\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\u5305\u542b\u8d85\u591a\u96f6\u4ee3\u7801\u5c0f\u5de5\u5177\uff0c\u4e0a\u4f20\u6570\u636e\u4e00\u952e\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\uff09<\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"border-bottom: 2px solid rgb(0, 150, 136);text-align: left;font-size: 12px;\" powered-by=\"xiumi.us\">\n<p><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]\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.35083798882681566\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_ocafb5YBQcZWdQRrtP2Xo7vaFWaecA.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYJyjlsib6bQ74Wibtria9gSC4sqocafb5YBQcZWdQRrtP2Xo7vaFWaecA\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"895\" style=\"\" data-recalc-dims=\"1\" \/><\/span><\/a><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3488888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_07T3ukOr5mxE6sbTMZvYNklUgT3oKg.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/YHGRXkSxjSSYqN0u6bwwXzLCBdlX9BXOYQlIrRTwqxXypnzYht7bhh3T07T3ukOr5mxE6sbTMZvYNklUgT3oKg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u70b9\u51fb\u201c\u9605\u8bfb\u539f\u6587\u201d\u8fdb\u5165\u7f51\u5740<\/p>\n<\/section>\n<section style=\"margin-left: 8%;margin-right: 8%;line-height: 1.1em;\" powered-by=\"xiumi.us\">\n<section style=\"width: 0px;display: inline-block;vertical-align: top;border-top: 1em solid rgb(0, 150, 136);border-left: 0.8em solid transparent !important;border-right: 0.8em solid transparent !important;\"><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 style=\"font-size: 11px;line-height: 0;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\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=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u4e0d\u53ef\u591a\u5f97\u7684GISTIC2.0\u6559\u5b66\u4e4bTCGA\u62f7\u8d1d\u6570\u53d8\u5f02CNV\u6570\u636e\u6574\u7406 \u5927\u6d77\u54e5 \u751f\u4fe1\u679c&nb […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=58764"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764\/revisions"}],"predecessor-version":[{"id":58777,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/58764\/revisions\/58777"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=58764"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=58764"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=58764"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}