{"id":24106,"date":"2024-01-10T17:24:55","date_gmt":"2024-01-10T09:24:55","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24106"},"modified":"2024-01-10T17:24:58","modified_gmt":"2024-01-10T09:24:58","slug":"%e5%88%9d%e6%8e%a2plink%e6%96%87%e4%bb%b6%e6%a0%bc%e5%bc%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24106","title":{"rendered":"\u521d\u63a2PLINK\u6587\u4ef6\u683c\u5f0f"},"content":{"rendered":"

\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76\uff08Genome-Wide Association Study\uff0cGWAS\uff09\u8fc5\u901f\u53d1\u5c55\uff0c\u4e3a\u63a2\u7d22\u75be\u75c5\u7684\u53d1\u75c5\u673a\u5236\u505a\u51fa\u4e86\u7a81\u51fa\u8d21\u732e\uff0c\u4e5f\u4e3a\u7cbe\u51c6\u533b\u5b66\u7684\u53d1\u5c55\u5960\u5b9a\u57fa\u7840\u3002\u5728\u8fdb\u884cGWAS\u5206\u6790\u65f6\uff0c\u7ecf\u5e38\u4f1a\u4f7f\u7528\u5230PLINK\u8f6f\u4ef6\uff0c\u5bf9\u4e8e\u65b0\u624b\u6765\u8bf4\u53ef\u80fd\u638c\u63e1\u8d77\u6765\u6bd4\u8f83\u56f0\u96be\uff0c<\/p>\n

PLINK\u662f\u4e00\u4e2a\u514d\u8d39\u7684\u5f00\u6e90\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u5206\u6790\u5de5\u5177\u96c6\uff0c\u65e8\u5728\u4ee5\u9ad8\u6548\u7387\u8ba1\u7b97\u7684\u65b9\u5f0f\u6267\u884c\u4e00\u7cfb\u5217\u57fa\u672c\u7684\u3001\u5927\u89c4\u6a21\u7684\u5206\u6790\u3002PLINK\u7684\u91cd\u70b9\u5206\u6790\u5bf9\u8c61\u662f\u57fa\u56e0\u578b\u6216\u8005\u8868\u578b\u6570\u636e\uff0c\u53ef\u4ee5\u4e3a\u540e\u7eed\u7684\u53ef\u89c6\u5316\u3001\u6ce8\u91ca\u548c\u7ed3\u679c\u5b58\u50a8\u63d0\u4f9b\u4e00\u4e9b\u652f\u6301\u3002<\/p>\n

\u30101\u3011\u5de5\u5177\u4e0b\u8f7d\uff1a<\/strong>https:\/\/www.cog-genomics.org\/plink2\/<\/a><\/p>\n

\u9996\u5148\u6211\u4eec\u6253\u5f00\u9875\u9762\uff0c\u786e\u5b9a\u597d\u54b1\u4eecWindows\u7684\u64cd\u4f5c\u7cfb\u7edf\uff08\u4e00\u822c\u90fd\u662f64\u4f4d\u7684\uff0c\u7ea2\u8272\u6807\u8bb0\u5904\uff09\uff0c\u70b9\u51fb\u201cdownload<\/strong>\u201d\u540e\u5f00\u59cb\u4e0b\u8f7d\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/p>\n

<\/p>\n

\u30102\u3011\u4f7f\u7528\u624b\u518c\uff1a<\/strong>https:\/\/zzz.bwh.harvard.edu\/plink\/index.shtml<\/p>\n

<\/p>\n

\u6240\u4ee5\u9996\u5148\u5c0f\u679c\u5c06\u548c\u5927\u5bb6\u5206\u4eabPLINK\u6587\u4ef6\u7684\u57fa\u672c\u683c\u5f0f\u3002\u5c0f\u679c\u5728\u8fd9\u91cc\u8bb2\u5230\u7684PLINK\u6587\u4ef6\u4e3b\u8981\u6709\u4e09\u7c7b\uff0c\u5373bed\u3001bim\u548cfam\u6587\u4ef6\u3002\u5176\u4e2dbed\u662f\u5b58\u50a8\u57fa\u56e0\u578b\u4fe1\u606f\u7684\uff0cbim\u6587\u4ef6\u5219\u662f\u5b58\u50a8\u6bcf\u4e2a\u9057\u4f20\u53d8\u5f02\uff08\u901a\u5e38\u662fSNP\uff09\u7684\u76f8\u5173\u4fe1\u606f\uff0c\u6700\u540e\u7684fam\u5b58\u50a8\u7684\u662f\u6837\u672c\u4fe1\u606f\uff0c\u63a5\u4e0b\u6765\u5c0f\u679c\u5c06\u4e00\u4e00\u4ecb\u7ecd\u3002<\/p>\n

\u8f93\u5165\u6587\u4ef6\u51c6\u5907<\/strong><\/p>\n

    \n
  1. ped<\/strong><\/li>\n<\/ol>\n

    1.1 ped \u5305\u542b\u6837\u672c\u7684\u8c31\u7cfb\u4fe1\u606f\u548c\u57fa\u56e0\u578b\u4fe1\u606f<\/p>\n

    1.2 ped \u5fc5\u987b\u4e0efam \u6587\u4ef6\u4e00\u8d77\uff0c\u524d6\u4e2a\u5b57\u6bb5\u4e0efam\u6587\u4ef6\u5bf9\u5e94<\/p>\n

    1.3 \u4f7f\u7528recode \u4ea7\u751fped\u6587\u4ef6<\/p>\n

    \u4e3e\u4f8b\uff1a\u6bcf\u4e00\u884c\u4e3a\u4e00\u4e2a\u6837\u672c<\/p>\n

    \u7b2c\u4e00\u5217 \u5bb6\u7cfb\u7f16\u53f7\uff08Family ID\uff09<\/p>\n

    \u7b2c\u4e8c\u5217 \u5bb6\u7cfb\u5185\u90e8\u7f16\u53f7\uff08Individual ID\uff09<\/p>\n

    \u7b2c\u4e09\u5217 \u7236\u7cfb\u7f16\u53f7 \uff08Paternal ID\uff09<\/p>\n

    \u7b2c\u56db\u5217 \u6bcd\u7cfb\u7f16\u53f7 \uff08Maternal ID\uff09<\/p>\n

    \u7b2c\u4e94\u5217 \u6027\u522b\u7f16\u53f7\uff08Sex \u30101=male\uff1b 2=female\uff1bother=unknown\u3011\uff09<\/p>\n

    \u7b2c\u516d\u5217 \u8868\u578b\u503c\uff08Phenotype\uff09<\/p>\n

      \n
    1. map<\/strong><\/li>\n<\/ol>\n

      \u4e3e\u4f8b\uff1a \u6587\u4ef6\u4e2d\u5fc5\u987b\u4e14\u4ec5\u5305\u542b\u56db\u5217<\/p>\n

      <\/p>\n

      \u7b2c\u4e00\u5217\u4ee3\u8868\u67d3\u8272\u4f53<\/p>\n

      \u7b2c\u4e8c\u5217\u4ee3\u8868snp\u7684\u540d\u79f0<\/p>\n

      \u7b2c\u4e09\u5217\u4ee3\u8868\u6469\u5c14\u8ddd\u79bb\uff0c\u4e00\u822c\u7528\u4e0d\u4e0a<\/p>\n

      \u7b2c\u56db\u5217\u4ee3\u8868\u7269\u7406\u8ddd\u79bb\uff0c\u8fd9\u4e2a\u6709\u7528\u7684<\/p>\n

        \n
      1. bed <\/strong><\/li>\n<\/ol>\n

        \u6587\u4ef6bed\u4e3b\u8981\u662f\u5b58\u50a8\u7b49\u4f4d\u57fa\u56e0\u4fe1\u606f\uff0c\u8be5\u683c\u5f0f\u7684\u6587\u4ef6\u4e3b\u8981\u5305\u542b\u4e86\u57fa\u56e0\u578b\u7684\u53cc\u7b49\u4f4d\u57fa\u56e0\u53d8\u5f02\u3002\u5fc5\u987b\u9644\u5e26.bim\u548c.fam\u6587\u4ef6\u3002\u7528–bfile\u52a0\u8f7d;\u53ef\u4ee5\u4f7f\u7528–make-bed\u547d\u4ee4\u751f\u6210\u3002\u6ce8\u610f\u7684\u662f\u8be5\u683c\u5f0f\u548c\u6211\u4eec\u5e73\u65f6\u63a5\u89e6\u542b\u6709\u57fa\u56e0\u7ec4\u4f4d\u7f6e\u7684bed\u683c\u5f0f\u6587\u4ef6\u4e0d\u540c\u3002\u5728\u57fa\u56e0\u578b\u4fe1\u606f\u4e2d\uff0c\u6bcf\u4e00\u884c\u662f\u4e00\u4e2a\u4e2a\u4f53\uff0c\u6bcf\u4e00\u5217\u5c31\u662f\u4e00\u4e2a\u53d8\u5f02\u3002\u5176\u4e2d0\u30011\u30012\u5206\u522b\u5bf9\u5e94\u4e86aa\u3001Aa\u6216aA\u548cAA\u3002<\/p>\n

          \n
        1. bim <\/strong><\/li>\n<\/ol>\n

          bim\u6587\u4ef6\u662f\u5b58\u50a8\u6bcf\u4e2a\u9057\u4f20\u53d8\u5f02\uff08\u901a\u5e38\u662fSNP\uff09\u7684\u76f8\u5173\u4fe1\u606f\u6587\u4ef6\uff0c\u662f\u4e00\u4e2a\u6ca1\u6709\u9898\u5934\u7684\u6587\u672c\u6587\u4ef6\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u9057\u4f20\u53d8\u5f02\uff0c\u5171\u8ba1\u67096\u5217\uff0c\u5176\u4fe1\u606f\u5982\u4e0b\uff1a<\/p>\n

          4.1 \u7b2c\u4e00\u5217\u662f\u67d3\u8272\u4f53\u4fe1\u606f<\/p>\n

          4.2 \u7b2c\u4e8c\u5217\u662fsnp\u7684\u540d\u5b57<\/p>\n

          4.3 \u7b2c\u4e09\u5217\u662f\u6469\u5c14\u8ddd\u79bb\uff0c\u53ef\u4ee5\u75280<\/p>\n

          4.4 \u7b2c\u56db\u5217\u662f\u7269\u7406\u8ddd\u79bb<\/p>\n

          4.5 \u7b2c\u4e94\u5217\u662f\u6b21\u8981\u7b49\u4f4d\u57fa\u56e0<\/p>\n

          4.6 \u7b2c\u516d\u5217\u662f\u4e3b\u8981\u7b49\u4f4d\u57fa\u56e0<\/p>\n

            \n
          1. fam <\/strong><\/li>\n<\/ol>\n

            \u5173\u4e8efam\u6587\u4ef6\uff0cfam\u5b58\u50a8\u7684\u662f\u6837\u672c\u4fe1\u606f\uff0c\u5b83\u4e5f\u662f\u4e00\u4e2a\u6ca1\u6709\u9898\u5934\u7684\u6587\u672c\u6587\u4ef6\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u6837\u672c\uff0c\u5171\u8ba16\u5217\uff0c\u5176\u4fe1\u606f\u5982\u4e0b\uff1a<\/p>\n

            5.1 fam\u6587\u4ef6\u8bb0\u5f55\u4e86\u6bcf\u4e2a\u6837\u672c\u5bb6\u7cfb\u7684\u4fe1\u606f<\/p>\n

            5.2 fam\u6587\u4ef6\u4e5f\u662f\u5fc5\u987b\u548cbed bim\u6587\u4ef6\u4e00\u8d77\u4f7f\u7528<\/p>\n

            5.3 \u4e3b\u8981\u67096 \u5217<\/p>\n

            \u5173\u4e8ePLINK\u6587\u4ef6\u7684\u57fa\u672c\u683c\u5f0f\u5c31\u4ecb\u7ecd\u5b8c\u6bd5\u4e86\uff0c\u5e0c\u671b\u5927\u5bb6\u80fd\u7262\u8bb0\u5404\u4e2a\u6587\u4ef6\u7684\u7ed3\u6784\u4fe1\u606f\uff0c\u8fd9\u5728\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u4e2d\u975e\u5e38\u91cd\u8981\u3002<\/p>\n

            \u6b22\u8fce\u4f7f\u7528\uff1a\u4e91\u751f\u4fe1\u751f\u7269\u4fe1\u606f\u5b66\u5e73\u53f0\uff08\u00a0\u00a0http:\/\/www.biocloudservice.com\/home.html<\/a>\uff09\uff0c\u4e86\u89e3\u66f4\u591a\u751f\u4fe1\u77e5\u8bc6\u4e0e\u6280\u5de7\u5206\u6790\u3002<\/p>\n

            \u8bf7\u671f\u5f85\u5c0f\u679c\u7684\u4e0b\u4e00\u671f\u5206\u4eab\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

            \u5168\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76\uff08Genome-Wide Association Study\uff0cGWAS\uff09\u8fc5\u901f\u53d1\u5c55\uff0c\u4e3a\u63a2\u7d22\u75be\u75c5\u7684 […]<\/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\/24106"}],"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=24106"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24106\/revisions"}],"predecessor-version":[{"id":24111,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24106\/revisions\/24111"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24106"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24106"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24106"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}