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src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_tPZ7jBicLmWwBBrKIXhHUzUo9327GA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXElq0pRjHGkvRXqswXNFKUNiaKetPZ7jBicLmWwBBrKIXhHUzUo9327GA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"919\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u8fd9\u91cc\u9009\u62e9\u5c0f\u4f19\u4f34\u81ea\u5df1\u7684\u57fa\u56e0\uff0c\u5c0f\u82b1\u5728\u8fd9\u91cc\u4f7f\u7528\u7684\u662f\u793a\u4f8b\u3002\u6ce8\u610fDataset\u6570\u636e\u96c6\u8fd9\u91cc\u9009\u62e9\u4e24\u4e2a\uff1a\u4e00\u822c\u662f<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.5820568927789935\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_2icY1OlS6PVym3SvCLkc2ufskZz6hg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXQiaFHVbEu0ZYTtdLBnDxxmJbus2icY1OlS6PVym3SvCLkc2ufskZz6hg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"457\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u8fd9\u4e24\u4e2a\uff0cFPKM\u6570\u636e\u3002\u63a5\u4e0b\u6765\u5c31\u662f\u53bb\u4e0b\u8f7d\u5566\uff1a\u70b9\u51fb\u4e0b\u4e00\u6b65\u5c31\u4f1a\u8fdb\u5230\u8fd9\u4e2a\u9875\u9762<\/p>\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=\"0.412962962962963\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_aticZoFnwN47VN15N4GDthDb6Zg2yg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXicG4FQ0WySa6uZH4wGfCXibDgJBaticZoFnwN47VN15N4GDthDb6Zg2yg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u70b9\u51fb\u53f3\u4e0a\u89d2\u7684\u4e0b\u8f7d\u5f97\u5230denseDataOnlyDownload.tsv \u8fd9\u6837\u7684\u6587\u4ef6<\/p>\n<p><br \/><\/p>\n<p>\u7136\u540e\u6211\u4eec\u8fd8\u9700\u8981\u4e00\u4e2a\u6587\u4ef6 \u662f450K\u7532\u57fa\u5316\u82af\u7247\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u8fd9\u4e2a\u6587\u4ef6\u5305\u542b\u6bcf\u4e2a\u7532\u57fa\u5316\u63a2\u9488\u7684\u4f4d\u7f6e\u7b49\u4fe1\u606f\u3002\u8fd9\u4e2a\u53ef\u4ee5\u4eceGEO\u6216\u8005xena\u4e0b\u8f7d\uff0c\u8fd9\u91cc\u5c0f\u82b1\u51c6\u5907\u4e86\u4e00\u4efd\u653e\u5728\u8fde\u63a5\u91cc\u9762illuminaMethyl450_hg38_GDC.txt<\/p>\n<p><br \/><\/p>\n<p>\u63a5\u4e0b\u6765\u5c31\u662f\u91cd\u5934\u620f\u4e86\uff0c\u6211\u4eec\u7528R\u8bed\u8a00\u53ef\u89c6\u5316\u57fa\u56e0\u7ec4\u7684\u4f4d\u7f6e\uff0c\u8fd9\u4e2a\u5185\u5bb9\u4e3b\u8981\u5305\u62ec\u542f\u52a8\u5b50TSS\u533a\u548c\u57fa\u56e0boby\u5185\u3002<\/p>\n<p>\u6ca1\u6709trackViewer\u5305\u7684\u5c0f\u4f19\u4f34\u9700\u8981\u81ea\u5df1\u4e0b\u8f7d\u4e00\u4e0b\u54e6\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"trackViewer\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(trackViewer) <span class=\"code-snippet__comment\">#\u4e3b\u8981\u753b\u56fe\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">methy <- read.delim(<span class=\"code-snippet__string\">\"denseDataOnlyDownload.tsv\"<\/span>) <span class=\"code-snippet__comment\">##\u8fd9\u91cc\u8bfb\u53d6Xena\u4e0b\u8f7d\u7684\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">anno <- read.delim(<span class=\"code-snippet__string\">\"illuminaMethyl450_hg38_GDC.txt\"<\/span>) <span class=\"code-snippet__comment\">##\u8bfb\u53d6\u7532\u57fa\u5316\u82af\u7247\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ddd <- anno %>% plotly::filter(X.id %in% colnames(methy))<\/span><\/code><code><span class=\"code-snippet_outer\">SNP <- ddd$chromStart<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(ddd$chromStart, width=<span class=\"code-snippet__number\">1<\/span>, <span class=\"code-snippet__built_in\">names<\/span>=ddd$X.id)) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u68d2\u68d2\u56fe\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(biomaRt)<\/span><\/code><code><span class=\"code-snippet_outer\">entrez=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"GAPDH\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">goids = getBM(<span class=\"code-snippet__built_in\">attributes<\/span> = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">'hgnc_symbol'<\/span>, <span class=\"code-snippet__string\">'chromosome_name'<\/span>,<span class=\"code-snippet__string\">\"start_position\"<\/span>,<span class=\"code-snippet__string\">\"end_position\"<\/span>,<span class=\"code-snippet__string\">\"strand\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">filters = <span class=\"code-snippet__string\">'hgnc_symbol'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">values = entrez,<\/span><\/code><code><span class=\"code-snippet_outer\">mart = ensembl)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (goids$strand== -<span class=\"code-snippet__number\">1<\/span>){<\/span><\/code><code><span class=\"code-snippet_outer\">features <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(<span class=\"code-snippet__built_in\">c<\/span>(goids$start_position,goids$end_position+<span class=\"code-snippet__number\">1<\/span>), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock\u8d77\u4f7f\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">width=<span class=\"code-snippet__built_in\">c<\/span>(goids$end_position-goids$start_position, <span class=\"code-snippet__number\">2000<\/span>), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock \u7684\u957f\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Gene\"<\/span>,<span class=\"code-snippet__string\">\"TSS\"<\/span>))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">features$fill <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"black\"<\/span>,<span class=\"code-snippet__string\">\"red\"<\/span>) <span class=\"code-snippet__comment\">#\u5757\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<span class=\"code-snippet__keyword\">else<\/span>{<\/span><\/code><code><span class=\"code-snippet_outer\">features <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(<span class=\"code-snippet__built_in\">c<\/span>(goids$start_position-<span class=\"code-snippet__number\">2001<\/span>,goids$start_position), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock\u8d77\u4f7f\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">width=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">2000<\/span>, goids$end_position-goids$start_position), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock \u7684\u957f\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"TSS\"<\/span>,<span class=\"code-snippet__string\">\"Gene\"<\/span>))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">features$fill <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"red\"<\/span>,<span class=\"code-snippet__string\">\"black\"<\/span>) <span class=\"code-snippet__comment\">#\u5757\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$color <- sample.int(<span class=\"code-snippet__built_in\">length<\/span>(SNP), <span class=\"code-snippet__built_in\">length<\/span>(SNP)) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u4e0a\u9762\u7684\u7403\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$border <- sample(<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"grey60\"<\/span>, <span class=\"code-snippet__string\">\"grey50\"<\/span>), <span class=\"code-snippet__built_in\">length<\/span>(SNP), replace=<span class=\"code-snippet__literal\">TRUE<\/span>) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$alpha <- 0.6 <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u900f\u660e\u5ea60-1\u4e4b\u95f4,sample\u662f\u751f\u6210100-200\u4e4b\u95f4\u7684\u968f\u673a\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$ce <- 0.5<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$label <- \"C\" #\u7403\u5185\u7684\u5b57\u7b26<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$label.col <- \"black\" #\u7403\u5185\u7684\u6807\u7b7e\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># features$height <- c(0.02, 0.05, 0.04) #\u5757\u7684\u9ad8\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$score <- sample.int(4, length(sample.gr), replace = TRUE) #\u8bbe\u7f6e\u7403\u7684\u6570\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">lolliplot(sample.gr, features,yaxis = <span class=\"code-snippet__built_in\">F<\/span>,ylab = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#yaxis\u8bbe\u7f6e\u4e0d\u663e\u793ay\u8f74<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>\u8fd9\u6837\u7ed3\u679c\u5c31\u51fa\u6765\u5566\uff01<\/p>\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=\"0.2709599027946537\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/5_410Qysy5Y5qMCEuhadLtcxeiaic22A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXapOqVuibvXQz8dCHVAjFwBH2GJB410Qysy5Y5qMCEuhadLtcxeiaic22A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"823\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u4e0b\u4e00\u6b65\u5462\uff0c\u6211\u4eec\u8fd8\u9700\u8981\u505a\u76f8\u5173\u6027\u5206\u6790\uff1a<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">results <- psych::corr.test(methy$ENSG00000111640.13,methy[<span class=\"code-snippet__number\">3<\/span>:(ncol(methy)-<span class=\"code-snippet__number\">1<\/span>)])<\/span><\/code><code><span class=\"code-snippet_outer\">results <- rbind(data.frame(results[[<span class=\"code-snippet__string\">\"r\"<\/span>]]),data.frame(results[[<span class=\"code-snippet__string\">\"p\"<\/span>]])) %>% t() %>% as.data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(results) <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"cor\"<\/span>,<span class=\"code-snippet__string\">\"p\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">r.cut <- 0.3<\/span><\/code><code><span class=\"code-snippet_outer\">results$color <- ifelse(results$cor> r.cut,<span class=\"code-snippet__string\">\"red\"<\/span>,ifelse(results$cor < -r.cut,<span class=\"code-snippet__string\">\"green\"<\/span>,<span class=\"code-snippet__string\">\"black\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">results$label <- ifelse(results$p > <span class=\"code-snippet__number\">0.05<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,ifelse(results$p ><span class=\"code-snippet__number\">0.01<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>ifelse(results$p><span class=\"code-snippet__number\">0.001<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>)))<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(ddd$chromStart, width=<span class=\"code-snippet__number\">1<\/span>, <span class=\"code-snippet__built_in\">names<\/span>= paste(ddd$X.id,results$label))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u68d2\u68d2\u56fe\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$border <- sample(<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"grey60\"<\/span>, <span class=\"code-snippet__string\">\"grey50\"<\/span>), <span class=\"code-snippet__built_in\">length<\/span>(SNP), replace=<span class=\"code-snippet__literal\">TRUE<\/span>) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$alpha <- 0.6 <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u900f\u660e\u5ea60-1\u4e4b\u95f4,sample\u662f\u751f\u6210100-200\u4e4b\u95f4\u7684\u968f\u673a\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$cex <- 0.5<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$color <- results$color <span class=\"code-snippet__comment\">#\u68d2\u5b50\u4e0a\u9762\u7684\u7403\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$label.col <- <span class=\"code-snippet__string\">\"black\"<\/span> <span class=\"code-snippet__comment\">#\u7403\u5185\u7684\u6807\u7b7e\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># features$height <- c(0.02, 0.05, 0.04) #\u5757\u7684\u9ad8\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$score <- sample.int(4, length(sample.gr), replace = TRUE) #\u8bbe\u7f6e\u7403\u7684\u6570\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">lolliplot(sample.gr, features,yaxis = <span class=\"code-snippet__built_in\">F<\/span>,ylab = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#yaxis\u8bbe\u7f6e\u4e0d\u663e\u793ay\u8f74<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>\u7ed3\u679c\uff1a<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0110803324099722\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/6_cuquiamCxSPI6WPVZPNHWichbCIcyQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXGWeQax1icfVXzUj4l8UZdVYPiaL9cuquiamCxSPI6WPVZPNHWichbCIcyQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"361\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: 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1.6;letter-spacing: 0px;padding-right: 6px;padding-left: 6px;\" powered-by=\"xiumi.us\">\n<p>\u5c0f\u4f19\u4f34\u770b\u5230\u8fd9\u6837\u7684\u5206\u6790\u662f\u4e0d\u662f\u5f88\u5fc3\u52a8\u5462\u3002\u5f53\u7136\u8981\u8bfe\u4e0b\u8981\u591a\u591a\u7406\u89e3\u7532\u57fa\u5316\uff0c\u4e0d\u80fd\u76f2\u76ee\u7684\u8ddf\u505a\u3002\u591a\u591a\u7406\u89e3\u4ee3\u7801\u7684\u610f\u601d\uff0c\u5c0f\u82b1\u5728\u4ee3\u7801\u540e\u9762\u4e5f\u6807\u8bb0\u4e86\u6ce8\u91ca\uff0c\u5c0f\u4f19\u4f34\u4eec\u8981\u597d\u597d\u53bb\u8bd5\u9a8c\u3002<\/p>\n<p>\u5feb\u52a8\u624b\u8bd5\u8bd5\u5427\uff01\uff01<\/p>\n<p><br \/><\/p>\n<p>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n<p><br \/><\/p>\n<p>\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/p>\n<\/section>\n<section style=\"text-align: right;justify-content: flex-end;display: flex;flex-flow: row;transform: translate3d(40px, 0px, 0px);margin-bottom: -40px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: auto;vertical-align: top;align-self: flex-start;flex: 0 0 auto;min-width: 5%;height: auto;\">\n<section style=\"transform: rotateZ(45deg);\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;\">\n<section style=\"display: inline-block;width: 26px;height: 26px;vertical-align: top;overflow: hidden;background-color: rgb(255, 255, 255);border-left: 1px solid rgb(160, 160, 160);border-bottom-left-radius: 0px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\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\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdt72DV7zqsmrNaiaaoOhic3sHzUpBN4r4MaBCk9p9v16yZwvMvS5nM7sQ\/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=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/8_pBN4r4MaBCk9p9v16yZwvMvS5nM7sQ.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdt72DV7zqsmrNaiaaoOhic3sHzUpBN4r4MaBCk9p9v16yZwvMvS5nM7sQ\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"895\" style=\"\" \/><\/span><\/a><br \/><\/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=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_uKaqczIP6EMQhkT9sW7c1bKv6z9AAg-6.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_jpg\/KDvR2NrGicSYCoxhZfqr5L0fxy3C9eSFdD9CpdQZl2iaySUTmNepgg2BpMuKaqczIP6EMQhkT9sW7c1bKv6z9AAg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"900\" style=\"\" \/><\/p>\n<p powered-by=\"xiumi.us\">\uff08\u70b9\u51fb\u9605\u8bfb\u539f\u6587\u8df3\u8f6c\uff09<\/p>\n<section style=\"text-align: left;margin: 10px 0%;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;min-width: 10%;vertical-align: top;padding-right: 20px;\">\n<section style=\"transform: translate3d(20px, 0px, 0px);margin: 10px 0% -30px;\" powered-by=\"xiumi.us\">\n<section style=\"color: rgb(62, 62, 62);text-align: justify;font-size: 12px;\">\n<p><strong><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-ratio=\"0.866\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/10_VX39fTfAHcwpbXZyWp605qaua3agkw.gif\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_gif\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXBGORDukajtv3omECibqv6mOtpVX39fTfAHcwpbXZyWp605qaua3agkw\/640?wx_fmt=gif'\" data-type=\"gif\" data-w=\"500\" height=\"15\" style=\"width: 18px;height: 15px;\" width=\"18\" \/> \u70b9\u4e00\u4e0b\u9605\u8bfb\u539f\u6587\u4e86\u89e3\u66f4\u591a\u8d44\u8baf<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 50px;height: 40px;vertical-align: top;overflow: hidden;\">\n<section style=\"text-align: center;margin-right: 0%;margin-left: 0%;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=\"0.7709090909090909\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_Uy8gkekjrwsLPVm3B59eXnlIlFQTog.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXYctobX6IgEG9R29oIicnE4lx7Uy8gkekjrwsLPVm3B59eXnlIlFQTog\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"275\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;margin-bottom: 24px;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"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>\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01 \u5c0f\u82b1 \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\/55315"}],"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=55315"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/55315\/revisions"}],"predecessor-version":[{"id":55328,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/55315\/revisions\/55328"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=55315"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=55315"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=55315"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}

{"id":55315,"date":"2024-06-16T16:25:29","date_gmt":"2024-06-16T08:25:29","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=55315"},"modified":"2024-06-16T16:25:29","modified_gmt":"2024-06-16T08:25:29","slug":"%e6%95%b2%e9%bb%91%e6%9d%bf%ef%bc%81%ef%bc%81%e5%b0%8f%e8%8a%b1%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e5%88%a9%e7%94%a8tcga%e6%95%b0%e6%8d%ae%e5%ba%93%e5%81%9a%e5%8d%95%e5%9f%ba%e5%9b%a0-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=55315","title":{"rendered":"\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01"},"content":{"rendered":"

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\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXCsT49aUEU6z8aJ1jjSbHUX4jYq80c3S3Vva8FlSORSyzyAvibXUdibnQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"946\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u5c0f\u82b1\u5728\u8fd9\u91cc\u5462\u4f7f\u7528LUAD\u7684\u6570\u636e\u7ed9\u5c0f\u4f19\u4f34\u505a\u6f14\u793a\u3002<\/p>\n<p>\u70b9\u51fb\u4e0b\u65b9\u7684to first variable<\/p>\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=\"0.8041349292709467\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_tPZ7jBicLmWwBBrKIXhHUzUo9327GA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXElq0pRjHGkvRXqswXNFKUNiaKetPZ7jBicLmWwBBrKIXhHUzUo9327GA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"919\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u8fd9\u91cc\u9009\u62e9\u5c0f\u4f19\u4f34\u81ea\u5df1\u7684\u57fa\u56e0\uff0c\u5c0f\u82b1\u5728\u8fd9\u91cc\u4f7f\u7528\u7684\u662f\u793a\u4f8b\u3002\u6ce8\u610fDataset\u6570\u636e\u96c6\u8fd9\u91cc\u9009\u62e9\u4e24\u4e2a\uff1a\u4e00\u822c\u662f<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.5820568927789935\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_2icY1OlS6PVym3SvCLkc2ufskZz6hg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXQiaFHVbEu0ZYTtdLBnDxxmJbus2icY1OlS6PVym3SvCLkc2ufskZz6hg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"457\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u8fd9\u4e24\u4e2a\uff0cFPKM\u6570\u636e\u3002\u63a5\u4e0b\u6765\u5c31\u662f\u53bb\u4e0b\u8f7d\u5566\uff1a\u70b9\u51fb\u4e0b\u4e00\u6b65\u5c31\u4f1a\u8fdb\u5230\u8fd9\u4e2a\u9875\u9762<\/p>\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=\"0.412962962962963\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_aticZoFnwN47VN15N4GDthDb6Zg2yg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXicG4FQ0WySa6uZH4wGfCXibDgJBaticZoFnwN47VN15N4GDthDb6Zg2yg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u7136\u540e\u70b9\u51fb\u53f3\u4e0a\u89d2\u7684\u4e0b\u8f7d\u5f97\u5230denseDataOnlyDownload.tsv \u8fd9\u6837\u7684\u6587\u4ef6<\/p>\n<p><br \/><\/p>\n<p>\u7136\u540e\u6211\u4eec\u8fd8\u9700\u8981\u4e00\u4e2a\u6587\u4ef6 \u662f450K\u7532\u57fa\u5316\u82af\u7247\u7684\u6ce8\u91ca\u4fe1\u606f\uff0c\u8fd9\u4e2a\u6587\u4ef6\u5305\u542b\u6bcf\u4e2a\u7532\u57fa\u5316\u63a2\u9488\u7684\u4f4d\u7f6e\u7b49\u4fe1\u606f\u3002\u8fd9\u4e2a\u53ef\u4ee5\u4eceGEO\u6216\u8005xena\u4e0b\u8f7d\uff0c\u8fd9\u91cc\u5c0f\u82b1\u51c6\u5907\u4e86\u4e00\u4efd\u653e\u5728\u8fde\u63a5\u91cc\u9762illuminaMethyl450_hg38_GDC.txt<\/p>\n<p><br \/><\/p>\n<p>\u63a5\u4e0b\u6765\u5c31\u662f\u91cd\u5934\u620f\u4e86\uff0c\u6211\u4eec\u7528R\u8bed\u8a00\u53ef\u89c6\u5316\u57fa\u56e0\u7ec4\u7684\u4f4d\u7f6e\uff0c\u8fd9\u4e2a\u5185\u5bb9\u4e3b\u8981\u5305\u62ec\u542f\u52a8\u5b50TSS\u533a\u548c\u57fa\u56e0boby\u5185\u3002<\/p>\n<p>\u6ca1\u6709trackViewer\u5305\u7684\u5c0f\u4f19\u4f34\u9700\u8981\u81ea\u5df1\u4e0b\u8f7d\u4e00\u4e0b\u54e6\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#BiocManager::install(\"trackViewer\")<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(trackViewer) <span class=\"code-snippet__comment\">#\u4e3b\u8981\u753b\u56fe\u5305<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">methy <- read.delim(<span class=\"code-snippet__string\">\"denseDataOnlyDownload.tsv\"<\/span>) <span class=\"code-snippet__comment\">##\u8fd9\u91cc\u8bfb\u53d6Xena\u4e0b\u8f7d\u7684\u6570\u636e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">anno <- read.delim(<span class=\"code-snippet__string\">\"illuminaMethyl450_hg38_GDC.txt\"<\/span>) <span class=\"code-snippet__comment\">##\u8bfb\u53d6\u7532\u57fa\u5316\u82af\u7247\u6ce8\u91ca\u4fe1\u606f<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">ddd <- anno %>% plotly::filter(X.id %in% colnames(methy))<\/span><\/code><code><span class=\"code-snippet_outer\">SNP <- ddd$chromStart<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(ddd$chromStart, width=<span class=\"code-snippet__number\">1<\/span>, <span class=\"code-snippet__built_in\">names<\/span>=ddd$X.id)) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u68d2\u68d2\u56fe\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">library(biomaRt)<\/span><\/code><code><span class=\"code-snippet_outer\">entrez=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"GAPDH\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">goids = getBM(<span class=\"code-snippet__built_in\">attributes<\/span> = <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">'hgnc_symbol'<\/span>, <span class=\"code-snippet__string\">'chromosome_name'<\/span>,<span class=\"code-snippet__string\">\"start_position\"<\/span>,<span class=\"code-snippet__string\">\"end_position\"<\/span>,<span class=\"code-snippet__string\">\"strand\"<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">filters = <span class=\"code-snippet__string\">'hgnc_symbol'<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">values = entrez,<\/span><\/code><code><span class=\"code-snippet_outer\">mart = ensembl)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">if<\/span> (goids$strand== -<span class=\"code-snippet__number\">1<\/span>){<\/span><\/code><code><span class=\"code-snippet_outer\">features <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(<span class=\"code-snippet__built_in\">c<\/span>(goids$start_position,goids$end_position+<span class=\"code-snippet__number\">1<\/span>), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock\u8d77\u4f7f\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">width=<span class=\"code-snippet__built_in\">c<\/span>(goids$end_position-goids$start_position, <span class=\"code-snippet__number\">2000<\/span>), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock \u7684\u957f\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"Gene\"<\/span>,<span class=\"code-snippet__string\">\"TSS\"<\/span>))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">features$fill <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"black\"<\/span>,<span class=\"code-snippet__string\">\"red\"<\/span>) <span class=\"code-snippet__comment\">#\u5757\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<span class=\"code-snippet__keyword\">else<\/span>{<\/span><\/code><code><span class=\"code-snippet_outer\">features <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(<span class=\"code-snippet__built_in\">c<\/span>(goids$start_position-<span class=\"code-snippet__number\">2001<\/span>,goids$start_position), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock\u8d77\u4f7f\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">width=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__number\">2000<\/span>, goids$end_position-goids$start_position), <span class=\"code-snippet__comment\"># \u8bbe\u7f6eblock \u7684\u957f\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__built_in\">names<\/span>=<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"TSS\"<\/span>,<span class=\"code-snippet__string\">\"Gene\"<\/span>))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u540d\u5b57<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">features$fill <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"red\"<\/span>,<span class=\"code-snippet__string\">\"black\"<\/span>) <span class=\"code-snippet__comment\">#\u5757\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$color <- sample.int(<span class=\"code-snippet__built_in\">length<\/span>(SNP), <span class=\"code-snippet__built_in\">length<\/span>(SNP)) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u4e0a\u9762\u7684\u7403\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$border <- sample(<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"grey60\"<\/span>, <span class=\"code-snippet__string\">\"grey50\"<\/span>), <span class=\"code-snippet__built_in\">length<\/span>(SNP), replace=<span class=\"code-snippet__literal\">TRUE<\/span>) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$alpha <- 0.6 <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u900f\u660e\u5ea60-1\u4e4b\u95f4,sample\u662f\u751f\u6210100-200\u4e4b\u95f4\u7684\u968f\u673a\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$ce <- 0.5<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$label <- \"C\" #\u7403\u5185\u7684\u5b57\u7b26<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$label.col <- \"black\" #\u7403\u5185\u7684\u6807\u7b7e\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># features$height <- c(0.02, 0.05, 0.04) #\u5757\u7684\u9ad8\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$score <- sample.int(4, length(sample.gr), replace = TRUE) #\u8bbe\u7f6e\u7403\u7684\u6570\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">lolliplot(sample.gr, features,yaxis = <span class=\"code-snippet__built_in\">F<\/span>,ylab = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#yaxis\u8bbe\u7f6e\u4e0d\u663e\u793ay\u8f74<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>\u8fd9\u6837\u7ed3\u679c\u5c31\u51fa\u6765\u5566\uff01<\/p>\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=\"0.2709599027946537\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/5_410Qysy5Y5qMCEuhadLtcxeiaic22A.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXapOqVuibvXQz8dCHVAjFwBH2GJB410Qysy5Y5qMCEuhadLtcxeiaic22A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"823\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p>\u4e0b\u4e00\u6b65\u5462\uff0c\u6211\u4eec\u8fd8\u9700\u8981\u505a\u76f8\u5173\u6027\u5206\u6790\uff1a<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"r\"><code><span class=\"code-snippet_outer\">results <- psych::corr.test(methy$ENSG00000111640.13,methy[<span class=\"code-snippet__number\">3<\/span>:(ncol(methy)-<span class=\"code-snippet__number\">1<\/span>)])<\/span><\/code><code><span class=\"code-snippet_outer\">results <- rbind(data.frame(results[[<span class=\"code-snippet__string\">\"r\"<\/span>]]),data.frame(results[[<span class=\"code-snippet__string\">\"p\"<\/span>]])) %>% t() %>% as.data.frame()<\/span><\/code><code><span class=\"code-snippet_outer\">colnames(results) <- <span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"cor\"<\/span>,<span class=\"code-snippet__string\">\"p\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">r.cut <- 0.3<\/span><\/code><code><span class=\"code-snippet_outer\">results$color <- ifelse(results$cor> r.cut,<span class=\"code-snippet__string\">\"red\"<\/span>,ifelse(results$cor < -r.cut,<span class=\"code-snippet__string\">\"green\"<\/span>,<span class=\"code-snippet__string\">\"black\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">results$label <- ifelse(results$p > <span class=\"code-snippet__number\">0.05<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,ifelse(results$p ><span class=\"code-snippet__number\">0.01<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>ifelse(results$p><span class=\"code-snippet__number\">0.001<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>,<span class=\"code-snippet__string\">\"\"<\/span>)))<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr <- GRanges(<span class=\"code-snippet__string\">\"chr17\"<\/span>, IRanges(ddd$chromStart, width=<span class=\"code-snippet__number\">1<\/span>, <span class=\"code-snippet__built_in\">names<\/span>= paste(ddd$X.id,results$label))) <span class=\"code-snippet__comment\"># \u8bbe\u7f6e\u68d2\u68d2\u56fe\u4f4d\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$border <- sample(<span class=\"code-snippet__built_in\">c<\/span>(<span class=\"code-snippet__string\">\"grey60\"<\/span>, <span class=\"code-snippet__string\">\"grey50\"<\/span>), <span class=\"code-snippet__built_in\">length<\/span>(SNP), replace=<span class=\"code-snippet__literal\">TRUE<\/span>) <span class=\"code-snippet__comment\">#\u68d2\u5b50\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$alpha <- 0.6 <span class=\"code-snippet__comment\">#\u8bbe\u7f6e\u900f\u660e\u5ea60-1\u4e4b\u95f4,sample\u662f\u751f\u6210100-200\u4e4b\u95f4\u7684\u968f\u673a\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$cex <- 0.5<\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$color <- results$color <span class=\"code-snippet__comment\">#\u68d2\u5b50\u4e0a\u9762\u7684\u7403\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sample.gr$label.col <- <span class=\"code-snippet__string\">\"black\"<\/span> <span class=\"code-snippet__comment\">#\u7403\u5185\u7684\u6807\u7b7e\u7684\u989c\u8272<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># features$height <- c(0.02, 0.05, 0.04) #\u5757\u7684\u9ad8\u5ea6<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># sample.gr$score <- sample.int(4, length(sample.gr), replace = TRUE) #\u8bbe\u7f6e\u7403\u7684\u6570\u91cf<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">lolliplot(sample.gr, features,yaxis = <span class=\"code-snippet__built_in\">F<\/span>,ylab = <span class=\"code-snippet__built_in\">F<\/span>) <span class=\"code-snippet__comment\">#yaxis\u8bbe\u7f6e\u4e0d\u663e\u793ay\u8f74<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"padding-right: 12px;padding-left: 12px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p>\u7ed3\u679c\uff1a<\/p>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.0110803324099722\" data-s=\"300,640\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-08-25_\u300c\u8f6c\u300d\u6572\u9ed1\u677f\uff01\uff01\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5229\u7528TCGA\u6570\u636e\u5e93\u505a\u5355\u57fa\u56e0\u7532\u57fa\u5316\u4f4d\u70b9\u5206\u6790\uff01\uff01\/6_cuquiamCxSPI6WPVZPNHWichbCIcyQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXGWeQax1icfVXzUj4l8UZdVYPiaL9cuquiamCxSPI6WPVZPNHWichbCIcyQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"361\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;margin-top: 10px;margin-bottom: 10px;line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.302158273381295\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_5nuM2kWDibXtnERpSJXhG2Zp8zzfsw.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/KDvR2NrGicSabAuxud22NwA0IMVATn4JXbm5TstNngvG5cpaH8Qn9UR5Cr5nuM2kWDibXtnERpSJXhG2Zp8zzfsw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"834\" style=\"vertical-align: middle;width: 100%;\" \/><\/section>\n<\/section>\n<p powered-by=\"xiumi.us\"><br \/><\/p>\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;width: 98%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;border-style: solid;border-width: 2px;border-color: rgb(160, 160, 160);padding: 27px;\">\n<section style=\"text-align: justify;line-height: 1.6;letter-spacing: 0px;padding-right: 6px;padding-left: 6px;\" powered-by=\"xiumi.us\">\n<p>\u5c0f\u4f19\u4f34\u770b\u5230\u8fd9\u6837\u7684\u5206\u6790\u662f\u4e0d\u662f\u5f88\u5fc3\u52a8\u5462\u3002\u5f53\u7136\u8981\u8bfe\u4e0b\u8981\u591a\u591a\u7406\u89e3\u7532\u57fa\u5316\uff0c\u4e0d\u80fd\u76f2\u76ee\u7684\u8ddf\u505a\u3002\u591a\u591a\u7406\u89e3\u4ee3\u7801\u7684\u610f\u601d\uff0c\u5c0f\u82b1\u5728\u4ee3\u7801\u540e\u9762\u4e5f\u6807\u8bb0\u4e86\u6ce8\u91ca\uff0c\u5c0f\u4f19\u4f34\u4eec\u8981\u597d\u597d\u53bb\u8bd5\u9a8c\u3002<\/p>\n<p>\u5feb\u52a8\u624b\u8bd5\u8bd5\u5427\uff01\uff01<\/p>\n<p><br \/><\/p>\n<p>\u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n<p><br \/><\/p>\n<p>\u5982\u679c\u60f3\u7528\u670d\u52a1\u5668\u53ef\u4ee5\u8054\u7cfb\u5fae\u4fe1\uff1a18502195490\uff08\u5feb\u6765\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u5427\uff01\uff09<\/p>\n<\/section>\n<section style=\"text-align: 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