{"id":260,"date":"2024-11-23T09:50:55","date_gmt":"2024-11-23T01:50:55","guid":{"rendered":"https:\/\/obagg.com\/index.php\/2024\/11\/23\/chipseeker%e7%bb%98%e5%9b%be%e5%87%bd%e6%95%b0%e5%80%9f%e7%94%a8\/"},"modified":"2024-11-23T09:50:55","modified_gmt":"2024-11-23T01:50:55","slug":"chipseeker%e7%bb%98%e5%9b%be%e5%87%bd%e6%95%b0%e5%80%9f%e7%94%a8","status":"publish","type":"post","link":"https:\/\/obagg.com\/index.php\/2024\/11\/23\/chipseeker%e7%bb%98%e5%9b%be%e5%87%bd%e6%95%b0%e5%80%9f%e7%94%a8\/","title":{"rendered":"ChIPseeker\u7ed8\u56fe\u51fd\u6570\u501f\u7528"},"content":{"rendered":"

\u65e5\u5e38\u778e\u63b0<\/h4>\n

\u2003\u2003\u5bf9\u4e8eChIP-seq<\/code>\u3001ATAC-seq<\/code>\u7b49\u8fd9\u6837\u6355\u83b7\u57fa\u56e0\u7ec4\u5bcc\u96c6\u533a\u57df(\u5373\u5206\u6790\u7ed3\u679c\u4e2dpeak<\/code>)\u7684\u6280\u672f\uff0c\u5927\u5bb6\u591a\u591a\u5c11\u5c11\u5e94\u8be5\u6709\u6240\u8033\u95fb\u3002\u5728\u5206\u6790\u8fd9\u7c7b\u6d4b\u5e8f\u6570\u636e\u7684\u65f6\u5019\uff0c\u5fc5\u4e0d\u53ef\u5c11\u7684\u6b65\u9aa4\u5c31\u662f\u5c06peak<\/code>\u6ce8\u91ca\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u4ee5\u4fbf\u4e86\u89e3peak<\/code>\u51fa\u73b0\u5728\u54ea\u4e9b\u57fa\u56e0\u7684\u5468\u8fb9\u533a\u57df\uff0c\u4ece\u800c\u53d1\u73b0\u751f\u7269\u5b66\u4e0a\u7684\u610f\u4e49\u3002\u76ee\u524d\uff0c\u6ce8\u91capeak<\/code>\u7684\u8f6f\u4ef6\u4e0d\u5728\u5c11\u6570\uff0c\u5982ChIPseeker<\/code>\u3001homer2<\/code>\u7b49\u3002\u4eca\u5929\u6211\u4eec\u4e3b\u8981\u6765\u8bf4\u8bf4\u5982\u4f55\u5229\u7528ChIPseeker<\/code>\u7ed8\u5236peak<\/code>\u7684\u5206\u5e03\u997c\u56fe\u548c\u6761\u5f62\u56fe\u3002<\/p>\n

\u6ce8\u91ca<\/h4>\n

\u2003\u2003ChIPseeker<\/code>\u7684\u7528\u6cd5\u76f8\u5f53\u7b80\u5355\uff0c\u8fd9\u91cc\u5c31\u987a\u4fbf\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\uff0c\u4e0b\u9762\u4f7f\u7528\u5305\u91cc\u9762\u7684\u6570\u636e\u6f14\u793a\u4e00\u4e0b\uff1a<\/p>\n

    \n
  1. \u4f7f\u7528R\u91cc\u9762\u7684\u6570\u636e\u5e93<\/li>\n<\/ol>\n
    library(ChIPseeker)\nlibrary(TxDb.Hsapiens.UCSC.hg19.knownGene)\nlibrary(org.Hs.eg.db)\n\nfiles <\/code><\/pre>\n
    \u2003\u2003\u5982\u4e0a\u9762\u6240\u793a\uff0c\u8c03\u7528\u4e00\u4e0bannotatePeak<\/code>\u51fd\u6570\u6ce8\u91ca\u5c31\u5b8c\u6210\u4e86\u3002\u5176\u4e2d\uff0cTxDb.Hsapiens.UCSC.hg19.knownGene<\/code>\u6570\u636e\u5e93\u662f\u5fc5\u987b\u7684\uff0corg.Hs.eg.db<\/code>\u6570\u636e\u5e93\u4e3a\u53ef\u9009\u9879\uff0c\u5982\u679c\u63d0\u4f9b\u4e86\u6ce8\u91ca\u7ed3\u679c\u91cc\u9762\u4f1a\u591a\u51faENSEMBL<\/code>\u3001SYMBOL<\/code>\u3001GENENAME<\/code>\u4e09\u5217\u4fe1\u606f\u3002\u5f53\u7136\uff0cannotatePeak<\/code>\u8fd8\u6709\u5176\u4ed6\u53c2\u6570\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8bbe\u7f6e\uff0c\u8fd9\u91cc\u5c31\u4e0d\u5c55\u793a\u4e86\u3002<\/p>\n
      \n
    1. \u4f7f\u7528gtf\u6587\u4ef6<\/li>\n<\/ol>\n
      library(GenomicFeatures)\n\ntxdb <\/code><\/pre>\n
      \u2003\u2003\u8fd9\u79cd\u65b9\u5f0f\u6ce8\u91ca\u8d77\u6765\u4e5f\u975e\u5e38\u65b9\u4fbf\u3002\u4e0d\u8bba\u4f7f\u7528\u54ea\u79cd\u6ce8\u91ca\u65b9\u6cd5\uff0c\u6700\u7ec8\u751f\u6210\u7684\u6ce8\u91ca\u7ed3\u679c\u90fd\u662f\u4ee5csAnno<\/code>\u7c7b\u5bf9\u8c61\u7684\u65b9\u5f0f\u5b58\u50a8\uff0c\u540e\u7eed\u64cd\u4f5c\u5c31\u53ef\u4ee5\u57fa\u4e8e\u8fd9\u4e2a\u5bf9\u8c61\u4e86\u3002<\/p>\n
      \u8fc7\u6ee4<\/h4>\n
      \u2003\u2003\u6ce8\u91ca\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u9700\u6c42\u5bf9\u5176\u8fdb\u884c\u8fc7\u6ee4\uff0c\u7b5b\u9009\u60f3\u5173\u6ce8\u7684\u533a\u57df\u6765\u770b\u770b\u5206\u5e03\u60c5\u51b5\uff0c\u6bd4\u5982\uff0c\u8fd9\u91cc\u53ea\u4fdd\u7559Promoter<\/code>\u3001Exon<\/code>\u3001Intron<\/code>\u4e09\u4e2a\u5927\u7c7b\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u770b\u51fa\u8fc7\u6ee4\u540e\u6bcf\u4e2aFeature<\/code>\u7684\u6bd4\u4f8b\u4f1a\u91cd\u65b0\u8ba1\u7b97\uff1a<\/p>\n
      annofilter <\/code><\/pre>\n
      \u2003\u2003\u5f53\u7136\uff0c\u5728\u8fc7\u6ee4\u4e4b\u524d\uff0c\u6211\u4eec\u8981\u5148\u77e5\u9053\u90fd\u6709\u54ea\u4e9b\u5217\u53ef\u4ee5\u7528\u6765\u8fc7\u6ee4\uff0c\u53ef\u4ee5\u4f7f\u7528\u4e0b\u9762\u7684\u547d\u4ee4\u6765\u67e5\u770b\uff1a<\/p>\n
      head(peakanno@anno)\nGRanges object with 6 ranges and 11 metadata columns:\n      seqnames          ranges strand |          V4        V5       annotation\n                   |        \n  [1]     chr1   815093-817883      * | MACS_peak_1    295.76 Promoter (2-3kb)\n  [2]     chr1 1243288-1244338      * | MACS_peak_2     63.19 Promoter (       \n  [1]         1    803451    812182       8732          2      284593\n  [2]         1   1243994   1247057       3064          1      126789\n  [3]         1   2976181   2980350       4170          2      440556\n  [4]         1   3547331   3566671      19341          2       49856\n  [5]         1   3816968   3832011      15044          1   100133612\n  [6]         1   6304252   6305638       1387          1      390992\n      transcriptId distanceToTSS\n            \n  [1]   uc001abt.4         -2911\n  [2]   uc001aed.3             0\n  [3]   uc001aka.3             0\n  [4]   uc001ako.3             0\n  [5]   uc001alg.3             0\n  [6]   uc009vly.2           613\n  -------\n  seqinfo: 24 sequences from hg19 genome\n<\/numeric><\/character><\/character><\/integer><\/integer><\/integer><\/integer><\/character><\/numeric><\/character><\/rle><\/iranges><\/rle><\/code><\/pre>\n
      \u53ef\u89c6\u5316<\/h4>\n
        \n
      1. barplot
        \n\u2003\u2003\u4f7f\u7528ChIPseeker<\/code>\u6ce8\u91ca\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u5176\u5185\u7f6e\u7684\u51fd\u6570plotAnnoBar<\/code>\u6765\u5c55\u793a\u6837\u672c\u7684peak<\/code>\u5206\u5e03\u60c5\u51b5\uff0c\u9002\u5408\u4e00\u4e2a\u6216\u591a\u4e2a\u6837\u672c\u3002\u8fd9\u91cc\u6211\u4eec\u9009\u53d6\u4e24\u4e2a\u6837\u672c\u6765\u6f14\u793a\uff1a<\/li>\n<\/ol>\n
        alist <\/code><\/pre>\n
        \u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n
        \n
        \n
        <\/div>\n<\/div>\n
        <\/div>\n<\/div>\n
          \n
        1. pieplot
          \n\u2003\u2003\u5355\u4e2a\u6837\u672c\u7684\u65f6\u5019\u4e5f\u53ef\u4ee5\u9009\u62e9\u997c\u56fe\u6765\u5c55\u793a\u7ed3\u679c\uff0c\u8c03\u7528\u51fd\u6570plotAnnoPie<\/code>\u5373\u53ef\u7ed8\u56fe\uff1a<\/li>\n<\/ol>\n
          plotAnnoPie(peakanno)\n<\/code><\/pre>\n
          \u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n
          \n
          \n
          <\/div>\n<\/div>\n
          <\/div>\n<\/div>\n
          \u53ef\u89c6\u5316\u51fd\u6570\u501f\u7528<\/h4>\n
          \u2003\u2003\u5176\u5b9e\uff0c\u6211\u4eec\u4e5f\u53ef\u4ee5\u53ea\u7528ChIPseeker<\/code>\u7684\u53ef\u89c6\u5316\u51fd\u6570\u6765\u5c55\u793a\u81ea\u5df1\u7684\u7ed3\u679c\u800c\u4e0d\u7528\u5176\u6765\u6ce8\u91ca\u3002\u5982\u679c\u6211\u4eec\u5df2\u7ecf\u6709\u4e86\u6ce8\u91ca\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u5c06\u7edf\u8ba1\u7ed3\u679c\u6574\u7406\u6210\u7c7b\u4f3c\u4e0a\u9762\u6240\u793a\u5c55\u793a\u7684Genomic Annotation Summary<\/code>\u6570\u636e\u6846\u683c\u5f0f\uff0c\u7136\u540e\u501f\u52a9ChIPseeker<\/code>\u5305\u7684\u7ed8\u56fe\u51fd\u6570\u6765\u7ed8\u56fe\uff1a<\/p>\n
            \n
          1. barplot<\/li>\n<\/ol>\n
            df1 <\/code><\/pre>\n
            \u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n
            \n
            \n
            <\/div>\n<\/div>\n
            <\/div>\n<\/div>\n
            \u2003\u2003\u5982\u679c\u89c9\u5f97\u8fd9\u4e2abarplot<\/code>\u98ce\u683c\u4e0d\u9519\uff0c\u60f3\u7528\u4e8e\u7ed8\u5236\u81ea\u5df1\u7684\u6570\u636e\uff0c\u501f\u7528\u4e00\u4e0b\u51fd\u6570\u662f\u4e0d\u662f\u5f88\u65b9\u9762\u5feb\u6377\u3002\u51c6\u5907\u6570\u636e\u7684\u65f6\u5019\u53ea\u9700\u6ce8\u610f\u4e24\u70b9\uff1a\u4e00\u662f\u5fc5\u987b\u6709Feature<\/code>\u3001Frequency<\/code>\u4e24\u5217\uff0c\u5217\u540d\u4e0d\u80fd\u9519\uff0c\u5206\u522b\u7528\u4e8e\u6307\u5b9a\u7c7b\u522b\u53ca\u6bd4\u4f8b\uff1b\u4e8c\u662fFeature<\/code>\u7684\u6570\u636e\u7c7b\u578b\u4e3afactor\u3002\u7b2c\u4e09\u5217\u505a\u4e3a\u6837\u672c\u5217\uff0c\u540d\u79f0\u968f\u610f\uff0c\u5982\u679c\u6ca1\u6709categoryColumn<\/code>\u8bbe\u7f6e\u4e3a1\u3002<\/p>\n
              \n
            1. pieplot
              \n\u2003\u2003\u51c6\u5907\u997c\u56fe\u6570\u636e\u65f6\uff0c\u53ea\u9700\u8981\u6709Feature<\/code>\u3001Frequency<\/code>\u4e24\u5217\u65e2\u53ef\uff0c\u6709\u6ca1\u6709\u5176\u4ed6\u5217\u4e0d\u4f1a\u5f71\u54cd\u7ed8\u56fe\uff1a<\/li>\n<\/ol>\n
              df1\n   Feature Frequency  sample\n1   intron 33.333333 sampleA\n2     exon 27.147766 sampleA\n3 promoter 30.240550 sampleA\n4      utr  9.278351 sampleA\n\ncol <\/code><\/pre>\n
              \u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n
              \n
              \n
              <\/div>\n<\/div>\n
              <\/div>\n<\/div>\n
                \n
              1. \u81ea\u5b9a\u4e49pieplot
                \n\u2003\u2003\u5176\u5b9e\uff0cChIPseeker<\/code>\u7ed8\u5236\u7684\u997c\u56fe\u4e2a\u4eba\u4e0d\u662f\u5f88\u559c\u6b22\uff0c\u6709\u4e24\u4e2a\u5c0f\u7684\u56e0\u7d20\u3002\u9996\u5148\uff0c\u5176\u7ed8\u5236\u997c\u56fe\u65f6\u4e0d\u662f\u57fa\u4e8eggplot2<\/code>\uff0c\u800c\u662f\u57fa\u4e8e\u57fa\u7840\u51fd\u6570pie<\/code>\uff0c\u6269\u5c55\u6027\u6ca1\u6709\u90a3\u4e48\u65b9\u4fbf\uff1b\u518d\u8005\uff0c\u7ed8\u51fa\u7684\u56fe\u548c\u56fe\u4f8b\u7684\u95f4\u8ddd\u6bd4\u8f83\u5927\u3002\u867d\u7136\u8fd9\u4e24\u70b9\u53ef\u4ee5\u5ffd\u7565\u4e0d\u8ba1\uff0c\u4f46\u662f\u5982\u679c\u80fd\u7ed8\u51fa\u66f4\u63a5\u8fd1\u6210\u54c1\u56fe\u7684\u6548\u679c\u90a3\u540e\u7eed\u4e0d\u662f\u66f4\u7701\u65f6\u7701\u529b\u4e48\u3002\u6240\u4ee5\uff0c\u4e2a\u4eba\u501f\u7528ChIPseeker<\/code>\u7684\u914d\u8272\u65b9\u6cd5\u5305\u88c5\u4e86\u4e00\u4e2a\u57fa\u4e8eggplot2<\/code>\u7684\u7ed8\u5236\u997c\u56fe\u7684\u51fd\u6570\uff0c\u53ef\u4ee5\u63a5\u53d7ChIPseeker<\/code>\u7684\u6ce8\u91ca\u5bf9\u8c61\u6216\u8005\u542b\u6709Feature<\/code>\u3001Frequency<\/code>\u4e24\u5217\u7684\u6570\u636e\u6846\u3002\u4e0b\u9762\u4e00\u8d77\u6765\u770b\u770b\u7ed8\u56fe\u6548\u679c\uff1a<\/li>\n<\/ol>\n
                plotpie <\/code><\/pre>\n
                \u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n
                \n
                \n
                <\/div>\n<\/div>\n
                <\/div>\n<\/div>\n
                \u7ed3\u675f\u8bed<\/h4>\n
                \u2003\u2003ChIPseeker<\/code>\u505a\u4e3aY\u53d4\u7684\u4f5c\u54c1\uff0c\u4f7f\u7528\u4f53\u9a8c\u4f9d\u7136\u662f\u987a\u6ed1\u6d41\u7545\u6ca1\u8bdd\u8bf4\uff0c\u529f\u80fd\u4e5f\u662f\u975e\u5e38\u5168\u9762\u5f3a\u5927\u3002\u7f51\u4e0a\u6709\u5f88\u591a\u5173\u4e8eChIPseeker<\/code>\u7684\u5e16\u5b50\uff0c\u8fd9\u91cc\u5217\u4e3e\u4e00\u4e2a\u672c\u4eba\u89c9\u5f97\u5199\u5f97\u6bd4\u8f83\u8be6\u7ec6\u7684\u5e16\u5b50\u53ef\u4f9b\u53c2\u8003\uff1ahttps:\/\/www.jianshu.com\/p\/c76e83e6fa57\u3002\u5de5\u6b32\u5584\u5176\u4e8b\u5fc5\u5148\u5229\u5176\u5668\uff0c\u597d\u7684\u5de5\u5177\u53ef\u4ee5\u8ba9\u6211\u4eec\u4e8b\u534a\u529f\u500d\uff0c\u8282\u7701\u66f4\u591a\u7684\u65f6\u95f4\u53bb\u5173\u6ce8\u6570\u636e\u672c\u8eab\u7684\u610f\u4e49\u3002\u4e0d\u8fc7\uff0c\u6ca1\u4e8b\u7684\u65f6\u5019\u5b66\u4e60\u4e00\u4e0b\u5de5\u5177\u7684\u539f\u7406\u53ca\u5b9e\u73b0\u8fc7\u7a0b\u8fd8\u662f\u6709\u597d\u5904\u7684\uff0c\u8fd9\u6837\u7528\u8d77\u6765\u624d\u4f1a\u66f4\u52a0\u5f97\u5fc3\u5e94\u624b\u6765\u53bb\u81ea\u5982\u3002\u597d\u4e86\uff0c\u4eca\u5929\u5230\u6b64\u7ed3\u675f~~~<\/p>\n
                <\/p>\n
                \u5f80\u671f\u56de\u987e<\/h4>\n
                \n
                R\u8bed\u8a00\u4e66\u7c4d\u514d\u8d39\u9886
                \n\u53ef\u89c6\u5316\uff1a\u7f51\u7edc\u56fe
                \n\u53ef\u89c6\u5316\uff1aWordcloud
                \n\u53ef\u89c6\u5316\uff1aDumbbell Chart
                \n\u53ef\u89c6\u5316\uff1aArc Diagrams<\/p>\n<\/blockquote>\n
                Please credit: OBA Blog<\/a> » ChIPseeker\u7ed8\u56fe\u51fd\u6570\u501f\u7528<\/a><\/p>","protected":false},"excerpt":{"rendered":"
                \u65e5\u5e38\u778e\u63b0 \u2003\u2003\u5bf9\u4e8eChIP-seq\u3001ATAC-seq\u7b49\u8fd9\u6837\u6355\u83b7\u57fa\u56e0\u7ec4\u5bcc\u96c6\u533a\u57df(\u5373\u5206\u6790\u7ed3\u679c\u4e2dpeak)\u7684\u6280\u672f\uff0c\u5927\u5bb6\u591a\u591a\u5c11\u5c11\u5e94\u8be5\u6709\u6240\u8033\u95fb\u3002\u5728\u5206\u6790\u8fd9\u7c7b\u6d4b\u5e8f\u6570\u636e\u7684\u65f6\u5019\uff0c\u5fc5\u4e0d\u53ef\u5c11\u7684\u6b65\u9aa4\u5c31\u662f\u5c06peak\u6ce8\u91ca\u5230\u57fa\u56e0\u7ec4\u4e0a\uff0c\u4ee5\u4fbf\u4e86\u89e3peak\u51fa\u73b0\u5728\u54ea\u4e9b\u57fa\u56e0\u7684\u5468\u8fb9\u533a\u57df\uff0c\u4ece\u800c\u53d1\u73b0\u751f\u7269\u5b66\u4e0a\u7684\u610f\u4e49\u3002\u76ee\u524d\uff0c\u6ce8\u91capeak\u7684\u8f6f\u4ef6\u4e0d\u5728\u5c11\u6570\uff0c\u5982ChIPseeker\u3001homer2\u7b49\u3002\u4eca\u5929\u6211\u4eec\u4e3b\u8981\u6765\u8bf4\u8bf4\u5982\u4f55\u5229\u7528ChIPseeker\u7ed8\u5236peak\u7684\u5206\u5e03\u997c\u56fe\u548c\u6761\u5f62\u56fe\u3002 \u6ce8\u91ca \u2003\u2003ChIPseeker\u7684\u7528\u6cd5\u76f8\u5f53\u7b80\u5355\uff0c\u8fd9\u91cc\u5c31\u987a\u4fbf\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\uff0c\u4e0b\u9762\u4f7f\u7528\u5305\u91cc\u9762\u7684\u6570\u636e\u6f14\u793a\u4e00\u4e0b\uff1a \u4f7f\u7528R\u91cc\u9762\u7684\u6570\u636e\u5e93 library(ChIPseeker) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) files \u2003\u2003\u5982\u4e0a\u9762\u6240\u793a\uff0c\u8c03\u7528\u4e00\u4e0bannotatePeak\u51fd\u6570\u6ce8\u91ca\u5c31\u5b8c\u6210\u4e86\u3002\u5176\u4e2d\uff0cTxDb.Hsapiens.UCSC.hg19.knownGene\u6570\u636e\u5e93\u662f\u5fc5\u987b\u7684\uff0corg.Hs.eg.db\u6570\u636e\u5e93\u4e3a\u53ef\u9009\u9879\uff0c\u5982\u679c\u63d0\u4f9b\u4e86\u6ce8\u91ca\u7ed3\u679c\u91cc\u9762\u4f1a\u591a\u51faENSEMBL\u3001SYMBOL\u3001GENENAME\u4e09\u5217\u4fe1\u606f\u3002\u5f53\u7136\uff0cannotatePeak\u8fd8\u6709\u5176\u4ed6\u53c2\u6570\u53ef\u4ee5\u6839\u636e\u9700\u8981\u8bbe\u7f6e\uff0c\u8fd9\u91cc\u5c31\u4e0d\u5c55\u793a\u4e86\u3002 \u4f7f\u7528gtf\u6587\u4ef6 library(GenomicFeatures) txdb \u2003\u2003\u8fd9\u79cd\u65b9\u5f0f\u6ce8\u91ca\u8d77\u6765\u4e5f\u975e\u5e38\u65b9\u4fbf\u3002\u4e0d\u8bba\u4f7f\u7528\u54ea\u79cd\u6ce8\u91ca\u65b9\u6cd5\uff0c\u6700\u7ec8\u751f\u6210\u7684\u6ce8\u91ca\u7ed3\u679c\u90fd\u662f\u4ee5csAnno\u7c7b\u5bf9\u8c61\u7684\u65b9\u5f0f\u5b58\u50a8\uff0c\u540e\u7eed\u64cd\u4f5c\u5c31\u53ef\u4ee5\u57fa\u4e8e\u8fd9\u4e2a\u5bf9\u8c61\u4e86\u3002 \u8fc7\u6ee4 \u2003\u2003\u6ce8\u91ca\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u9700\u6c42\u5bf9\u5176\u8fdb\u884c\u8fc7\u6ee4\uff0c\u7b5b\u9009\u60f3\u5173\u6ce8\u7684\u533a\u57df\u6765\u770b\u770b\u5206\u5e03\u60c5\u51b5\uff0c\u6bd4\u5982\uff0c\u8fd9\u91cc\u53ea\u4fdd\u7559Promoter\u3001Exon\u3001Intron\u4e09\u4e2a\u5927\u7c7b\u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u770b\u51fa\u8fc7\u6ee4\u540e\u6bcf\u4e2aFeature\u7684\u6bd4\u4f8b\u4f1a\u91cd\u65b0\u8ba1\u7b97\uff1a annofilter \u2003\u2003\u5f53\u7136\uff0c\u5728\u8fc7\u6ee4\u4e4b\u524d\uff0c\u6211\u4eec\u8981\u5148\u77e5\u9053\u90fd\u6709\u54ea\u4e9b\u5217\u53ef\u4ee5\u7528\u6765\u8fc7\u6ee4\uff0c\u53ef\u4ee5\u4f7f\u7528\u4e0b\u9762\u7684\u547d\u4ee4\u6765\u67e5\u770b\uff1a head(peakanno@anno) GRanges object with 6 ranges and 11 metadata columns: seqnames ranges strand | V4 V5 annotation | [1] chr1 815093-817883 * | MACS_peak_1 295.76 Promoter (2-3kb) [2] chr1 1243288-1244338 * | MACS_peak_2 63.19 Promoter ( [1] 1 803451 812182 8732 2 284593 [2] 1 1243994 1247057 3064 1 126789 [3] 1 2976181 2980350 4170 2 440556 [4] 1 3547331 3566671 19341 2 49856 [5] 1 3816968 3832011 15044 1 100133612 [6] 1 6304252 6305638 1387 1 390992 transcriptId distanceToTSS [1] uc001abt.4 -2911 [2] uc001aed.3 0 [3] uc001aka.3 0 [4] uc001ako.3 0 [5] uc001alg.3 0 [6] uc009vly.2 613 ——- seqinfo: 24 sequences from hg19 genome \u53ef\u89c6\u5316 barplot […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-260","post","type-post","status-publish","format-standard","hentry","category-share"],"_links":{"self":[{"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/posts\/260","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/comments?post=260"}],"version-history":[{"count":0,"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/posts\/260\/revisions"}],"wp:attachment":[{"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/media?parent=260"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/categories?post=260"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/obagg.com\/index.php\/wp-json\/wp\/v2\/tags?post=260"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}