{"id":323,"date":"2018-04-12T20:58:02","date_gmt":"2018-04-12T12:58:02","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=323"},"modified":"2021-01-08T20:48:17","modified_gmt":"2021-01-08T12:48:17","slug":"deseq2%e4%bd%bf%e7%94%a8%e6%b5%81%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=323","title":{"rendered":"DESeq2\u4f7f\u7528\u6d41\u7a0b"},"content":{"rendered":"<pre>\r\nlibrary(\"DESeq2\")\r\ndatabase <- read.table(file = \"COS_genes.count_table.xls\", sep = \"\\t\", header = T, row.names = 1)\r\ncountData <- database[,1:15]\r\ncondition <- factor(c(rep(\"COS0\",3),rep(\"COS1\",3),rep(\"COS3\",3),rep(\"COS6\",3),rep(\"COS12\",3)), levels = c(\"COS0\", \"COS1\",\"COS3\",\"COS6\",\"COS12\"))\r\ncountData <- round(as.matrix(countData))\r\ncoldata <- data.frame(row.names = colnames(countData), condition)\r\ndds <- DESeqDataSetFromMatrix(countData, DataFrame(condition), design= ~ condition )\r\ndds <- dds[ rowSums(counts(dds)) > 1, ]\r\ndds <- DESeq(dds)\r\nres0vs1 <- results(dds, contrast = c(\"condition\",\"COS1\",\"COS0\"))\r\ntable(res0vs1$pvalue <0.001)\r\nres0vs1 <- res0vs1[order(res0vs1$pvalue),]\r\nwrite.table(as.data.frame(res0vs1), file=\"res0vs1.xls\", sep=\"\\t\", quote = F)\r\n#\u753b\u56fe\r\nlibrary(geneplotter)\r\nplotMA(res0vs1, main=\"DESeq2\", ylim=c(-2,2))\r\n\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>library(&#8220;DESeq2&#8221;) database<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/323"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=323"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/323\/revisions"}],"predecessor-version":[{"id":670,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/323\/revisions\/670"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=323"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=323"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=323"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}