{"id":29196,"date":"2024-02-21T17:33:25","date_gmt":"2024-02-21T09:33:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29196"},"modified":"2024-02-21T17:33:26","modified_gmt":"2024-02-21T09:33:26","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%e5%ae%8c%e6%88%90%e4%bb%8e%e6%95%b0%e6%8d%ae%e4%b8%8b%e8%bd%bd%e5%88%b0%e5%85%8d%e7%96%ab%e6%b5%b8%e6%b6%a6ssgsea%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29196","title":{"rendered":"\u4e24\u5206\u949f\u5b8c\u6210\u4ece\u6570\u636e\u4e0b\u8f7d\u5230\u514d\u75ab\u6d78\u6da6ssGSEA\u5206\u6790"},"content":{"rendered":"

\u4eca\u5929\u5c0f\u679c\u5206\u4eab\u4e00\u4e0b\u514d\u75ab\u6d78\u6da6ssGESA\u5206\u6790\uff0c\u4ece\u6570\u636e\u4e0b\u8f7d\u5230\u5206\u6790\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

    \n
  1. \u5b89\u88c5\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

    install.packages(\u201cggplot2\u201d)<\/p>\n

    Install.packages(\u201ctidyverse\u201d)<\/p>\n

    install.packages(\u201cGSVA\u201d)<\/p>\n

    install.packages(\u201cpheatmap\u201d)<\/p>\n

      \n
    1. \u8f7d\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(ggplot2)<\/p>\n

      library(tidyverse)<\/p>\n

      library(GSVA)<\/p>\n

      library(pheatmap)<\/p>\n

        \n
      1. \u6570\u636e\u4e0b\u8f7d<\/li>\n<\/ol>\n

        \u5728Xena\u6570\u636e\u5e93\u4e0b\u8f7d\u8868\u8fbe\u77e9\u9635\u548cID\u5bf9\u5e94\u8868\u683c<\/p>\n

        #\u8868\u8fbe\u77e9\u9635\u4e0b\u8f7d<\/p>\n

        wget https:\/\/gdc-hub.s3.us-east-1.amazonaws.com\/download\/TCGA-KIRC.htseq_fpkm.tsv.gz<\/a><\/p>\n

        #\u57fa\u56e0ID\u8f6c\u5316\u5217\u8868<\/p>\n

        wget https:\/\/gdc-hub.s3.us-east-1.amazonaws.com\/download\/gencode.v22.annotation.gene.probeMap<\/a><\/p>\n

          \n
        1. \u4ee3\u7801\u5c55\u793a<\/li>\n<\/ol>\n

          #\u57fa\u56e0ID\u8f6c\u6362<\/p>\n

          expr<-read.table(“TCGA-KIRC.tsv”,header=T,sep=”\\t”,row.names=1)<\/p>\n

          geneann<-read.table(“gencode.v22.annotation.gene.probeMap”,header=T,sep=”\\t”,row.names=1)<\/p>\n

          expr$gsym <- geneann[rownames(expr),]$gene<\/p>\n

          expr<-distinct(expr,gsym,.keep_all=T)<\/p>\n

          row.names(expr)<-expr$gsym<\/p>\n

          expr<-slect(expr,-gsym)<\/p>\n

          write.table(expr,”TCGA-KIRC-expr.txt”,col.names=T,row.names=T,sep=”\\t”)<\/p>\n

          #ssGSEA\u5206\u6790<\/p>\n

          exp<-read.table(“TCGA-KIRC-expr.txt”,header=T,row.names=1,sep=”\\t”)<\/p>\n

          geneset<-read.table(“genelist.txt”,header=T,sep=”\\t”)<\/p>\n

          \u6784\u5efa\u514d\u75ab\u7ec6\u80deMarker\u57fa\u56e0\u96c6\uff1a<\/p>\n

          geneset2 <- split(geneset$Metagene,geneset$Cell.type)<\/p>\n

          #ssGSEA\uff1a<\/p>\n

          res <- gsva(as.matrix(exp),<\/p>\n

          geneset2,<\/p>\n

          method = “ssgsea”,<\/p>\n

          kcdf = “Gaussian”,<\/p>\n

          mx.diff = F,<\/p>\n

          verbose = F)<\/p>\n

          #\u7ed9\u70ed\u56fe\u6dfb\u52a0\u6837\u672c\u6ce8\u91ca\u4fe1\u606f\uff1a<\/p>\n

          group_list <- ifelse(str_sub(colnames(res),14,15) < 10,”tumor”,”normal”)<\/p>\n

          annotation <- data.frame(group_list)<\/p>\n

          rownames(annotation) <- colnames(res)<\/p>\n

          pheatmap(res,<\/p>\n

          show_colnames = F,<\/p>\n

          annotation_col = annotation,<\/p>\n

          fontsize = 10\uff0c<\/p>\n

          filename=\u201dssGSEA.pdf\u201d)<\/p>\n

          \"Dingtalk_20230228150544\"<\/p>\n

          \u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\uff0c\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

          \u4eca\u5929\u5c0f\u679c\u5206\u4eab\u4e00\u4e0b\u514d\u75ab\u6d78\u6da6ssGESA\u5206\u6790\uff0c\u4ece\u6570\u636e\u4e0b\u8f7d\u5230\u5206\u6790\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a \u5b89\u88c5\u9700\u8981\u7684R\u5305 install.pac […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","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\/29196"}],"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=29196"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29196\/revisions"}],"predecessor-version":[{"id":29198,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29196\/revisions\/29198"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29196"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29196"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29196"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}