{"id":29041,"date":"2024-02-20T17:41:01","date_gmt":"2024-02-20T09:41:01","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29041"},"modified":"2024-02-20T17:41:02","modified_gmt":"2024-02-20T09:41:02","slug":"%e5%88%a9%e7%94%a8r%e8%af%ad%e8%a8%80%e8%bf%9b%e8%a1%8censembl-id%e8%bd%ac%e6%8d%a2%e4%b8%bagene-name","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29041","title":{"rendered":"\u5229\u7528R\u8bed\u8a00\u8fdb\u884cEnsembl ID\u8f6c\u6362\u4e3aGene name"},"content":{"rendered":"

\u4eca\u5929\u5728\u505assGESA\u5206\u6790\u7684\u65f6\u5019\u53d1\u73b0\uff0cTCGA\u4e0b\u8f7d\u7684\u57fa\u56e0ID\u4e3aEnsembl ID,\u4e0b\u8f7d\u7684\u57fa\u56e0\u96c6\u4e3aGene name,\u5728\u505a\u5206\u6790\u4e4b\u524d\u8981\u505a\u4e00\u4e0b\u57fa\u56e0ID\u8f6c\u5316\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n

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

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

      \n
    1. \u5bfc\u5165\u9700\u8981\u7684R\u5305<\/li>\n<\/ol>\n

      library(tidyverse)<\/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

        4.\u4ee3\u7801\u5c55\u793a<\/p>\n

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

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

        \"Dingtalk_20230227122737\"<\/p>\n

        #ID\u548cGene symbol\u5bf9\u5e94\u5217\u8868<\/p>\n

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

        \"Dingtalk_20230227122946\"<\/p>\n

        #\u4e8c\u8005ID\u8fdb\u884c\u5339\u914d\uff0c\u5e76\u6dfb\u52a0\u4e00\u5217gsym<\/p>\n

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

        #\u53bb\u9664\u91cd\u590d\u7684Gene name<\/p>\n

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

        #\u5c06\u884c\u540d\u6539\u4e3aGene name<\/p>\n

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

        #\u5c06\u6dfb\u52a0\u7684gsym\u8fd9\u4e00\u5217\u5220\u9664<\/p>\n

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

        #\u5c06\u4fee\u6539\u7684\u7ed3\u679c\u6587\u4ef6\u4fdd\u5b58<\/p>\n

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

        \"Dingtalk_20230227123726\"<\/p>\n

        \u6700\u7ec8\u5c06Ensembl ID\u8f6c\u5316\u4e3agene name,\u6709\u9700\u8981\u7684\u53ef\u4ee5\u501f\u9274\u5b66\u4e60\uff0c\u5728\u8fd9\u91cc\u9700\u8981\u6ce8\u610f\u7684\u662f\u591a\u4e2aEnsembl ID\u5bf9\u5e94\u4e00\u4e2aGene name,\u5c0f\u679c\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

        \u4eca\u5929\u5728\u505assGESA\u5206\u6790\u7684\u65f6\u5019\u53d1\u73b0\uff0cTCGA\u4e0b\u8f7d\u7684\u57fa\u56e0ID\u4e3aEnsembl ID,\u4e0b\u8f7d\u7684\u57fa\u56e0\u96c6\u4e3aGene na […]<\/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\/29041"}],"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=29041"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29041\/revisions"}],"predecessor-version":[{"id":29045,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29041\/revisions\/29045"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29041"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29041"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29041"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}