{"id":236,"date":"2024-04-27T09:16:41","date_gmt":"2024-04-27T01:16:41","guid":{"rendered":"http:\/\/www.alearnerlin.top\/?p=236"},"modified":"2024-04-27T09:18:15","modified_gmt":"2024-04-27T01:18:15","slug":"twosamplemr%e6%9b%b4%e6%96%b0%e5%95%a6%ef%bc%81%ef%bc%81%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.alearnerlin.top\/index.php\/2024\/04\/27\/twosamplemr%e6%9b%b4%e6%96%b0%e5%95%a6%ef%bc%81%ef%bc%81%ef%bc%81\/","title":{"rendered":"TwoSampleMR\u66f4\u65b0\u5566\uff01\uff01\uff01"},"content":{"rendered":"

TwoSampleMR\u5305\u8fce\u6765\u4e860.6.0\u7248\u672c<\/h1>\n

\u4e4b\u524d\u5728opengwas\u4e2d\u7f51\u7ad9\u5c31\u770b\u5230\u6d88\u606f\uff0c5\u67081\u53f7\u4e4b\u540e\u9700\u8981\u4f7f\u7528opengwas\u7684api token\u624d\u53ef\u4ee5\u83b7\u53d6\u5230\u4ed6\u4eec\u7684gwas\u6570\u636e\u4e86\u3002
\n\u6628\u5929\u5bf9\u5305\u8fdb\u884c\u66f4\u65b0\u65f6\uff0c\u53d1\u73b0\u7248\u672c\u5df2\u7ecf\u53d8\u6210\u4e860.6.0\u7248\u672c\u3002\u73b0\u5728\u901a\u5e38\u4f7f\u7528\u7684 extract_instruments<\/code> \u51fd\u6570\u591a\u4e86\u4e00\u4e2a\u53c2\u6570\uff1a
\n\u8bf4\u660e\u5982\u4e0b\uff1a
\nopengwas_jwt\uff1aUsed to authenticate protected endpoints. Login to https:\/\/api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.<\/code><\/p>\n

\u5982\u679c\u76f4\u63a5\u4f7f\u7528extract_instruments<\/code>\u51fd\u6570\u7684\u8bdd\uff0c\u4f1a\u62a5\u9519<\/p>\n

exposure <- extract_instruments(outcomes='ukb-b-15926',\n+                                 p1 = 5e-08,\n+                                 clump = TRUE,\n+                                 p2 = 5e-08,\n+                                 r2 = 0.001,\n+                                 kb = 10000,\n+                                 )\nError in if (nrow(d) == 0) return(NULL) : \u53c2\u6570\u957f\u5ea6\u4e3a\u96f6<\/code><\/pre>\n
\u6211\u4eec\u5c31\u6309\u7167\u4ee5\u4e0a\u7684\u8bf4\u660e\u6765\u8fdb\u884c\u914d\u7f6e\u5427\uff01<\/p>\n
\u9996\u5148\u8fdb\u5165\u4e0a\u9762\u7684\u7f51\u7ad9:https:\/\/api.opengwas.io<\/a><\/p>\n
\u8fdb\u53bb\u4e4b\u540e\u8ba9\u4f60\u9009\u62e9\u4e24\u4e2a\u767b\u5f55\u65b9\u5f0f\uff0c\u8fd9\u91cc\u9009\u62e9\u4e24\u8005\u5747\u53ef\u3002<\/p>\n
\u4e4b\u540e\u5176\u4f1a\u81ea\u52a8\u751f\u6210\u4e00\u4e2atoken
\n
\"\"<\/div>
\n\u6ce8\u610f\uff01\uff01\uff01\u4e00\u5b9a\u8981\u5c06\u8fd9\u4e2atoken\u4fdd\u5b58\u5230\u4e00\u4e2atxt\u6587\u6863\u6216\u8005\u4e0d\u5bb9\u6613\u9057\u6f0f\u7684\u5730\u65b9\uff0c\u4e0d\u7136\u4e4b\u540e\u9700\u8981\u91cd\u65b0\u8bbe\u7f6e<\/strong><\/p>\n
\u7136\u540e\u6211\u4eec\u6253\u5f00Rstudio
\n\u8f93\u5165Sys.setenv(OPENGWAS_JWT = "your_token")<\/code>
\n\u5f15\u53f7\u5185\u7684\u5185\u5bb9\u6362\u6210\u7f51\u7ad9\u63d0\u4f9b\u7684token<\/p>\n
\u8fd0\u884c\u4e00\u4e0b\u547d\u4ee4ieugwasr::get_opengwas_jwt()<\/code>
\n
\"\"<\/div>
\n\u53d1\u73b0\u53ef\u4ee5\u8fd4\u56detoken\u503c\uff0c\u8fd9\u91cc\u6211\u4eec\u5c31\u914d\u7f6e\u597d\u5566\u3002<\/p>\n
\u73b0\u5728\u6211\u4eec\u7684\u51fd\u6570\u5c31\u53ef\u4ee5\u66f4\u6539\u4e3a\u8fd9\u6837\u4e86<\/p>\n
exposure <- extract_instruments(outcomes='ukb-b-15926',\n                                p1 = 5e-08,\n                                clump = TRUE,\n                                p2 = 5e-08,\n                                r2 = 0.001,\n                                kb = 10000,\n                                opengwas_jwt =ieugwasr::get_opengwas_jwt())<\/code><\/pre>\n
\u8fd0\u884c\u4e4b\u540e\u5c31\u53ef\u4ee5\u6b63\u5e38\u7684\u83b7\u53d6\u6570\u636e\u5566\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"
TwoSampleMR\u5305\u8fce\u6765\u4e860.6.0\u7248\u672c \u4e4b\u524d\u5728opengwas\u4e2d\u7f51\u7ad9\u5c31\u770b\u5230\u6d88\u606f\uff0c5\u67081\u53f7\u4e4b\u540e\u9700\u8981\u4f7f\u7528op […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11,6],"tags":[],"class_list":["post-236","post","type-post","status-publish","format-standard","hentry","category-r","category-6"],"_links":{"self":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/236","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/comments?post=236"}],"version-history":[{"count":1,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/236\/revisions"}],"predecessor-version":[{"id":239,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/posts\/236\/revisions\/239"}],"wp:attachment":[{"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/media?parent=236"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/categories?post=236"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.alearnerlin.top\/index.php\/wp-json\/wp\/v2\/tags?post=236"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}