{"id":61513,"date":"2024-10-30T15:36:26","date_gmt":"2024-10-30T07:36:26","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61513"},"modified":"2024-10-30T15:36:26","modified_gmt":"2024-10-30T07:36:26","slug":"dirichletmultinomial%e5%8c%85%ef%bc%9aai%e5%88%86%e6%9e%90%e5%be%ae%e7%94%9f%e7%89%a9%e7%bb%84%e6%95%b0%e6%8d%ae%e6%96%b0%e6%bd%ae%e6%b5%81%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61513","title":{"rendered":"DirichletMultinomial\u5305\uff1aAI\u5206\u6790\u5fae\u751f\u7269\u7ec4\u6570\u636e\u65b0\u6f6e\u6d41\uff01"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>\u55e8\uff0c\u63a2\u7d22\u8005\u4eec\uff0c\u5c0f\u679c\u5411\u5bfc\u518d\u6b21\u6b22\u8fce\u4f60\u4eec\uff01\u4eca\u5929\uff0c\u6211\u4eec\u7684\u63a2\u9669\u76ee\u7684\u5730\u662f\u795e\u79d8\u800c\u53c8\u590d\u6742\u7684\u5fae\u751f\u7269\u7ec4\u4e16\u754c\u3002\u5728\u8fd9\u4e2a\u4e16\u754c\u91cc\uff0c\u6bcf\u4e00\u4e2a\u5fae\u751f\u7269\u90fd\u626e\u6f14\u7740\u5176\u72ec\u7279\u7684\u89d2\u8272\uff0c\u800c\u5b83\u4eec\u4e4b\u95f4\u9519\u7efc\u590d\u6742\u7684\u76f8\u4e92\u4f5c\u7528\u6784\u6210\u4e86\u4e00\u4e2a\u5e9e\u5927\u7684\u7f51\u7edc\u3002\u4e3a\u4e86\u66f4\u597d\u5730\u7406\u89e3\u8fd9\u4e2a\u7f51\u7edc\uff0c\u6211\u4eec\u9700\u8981\u4e00\u628a\u5f3a\u5927\u7684\u5de5\u5177\u2014\u2014\u90a3\u5c31\u662fDirichletMultinomial\u5305\u3002<\/p>\n\n\n\n<p>\u5fae\u751f\u7269\u7ec4\u6570\u636e\uff0c\u5145\u6ee1\u4e86\u672a\u77e5\u548c\u6311\u6218\uff0c\u4f46\u540c\u65f6\u4e5f\u8574\u85cf\u7740\u65e0\u9650\u7684\u53ef\u80fd\u6027\u3002\u901a\u8fc7\u5206\u6790\u8fd9\u4e9b\u6570\u636e\uff0c\u6211\u4eec\u53ef\u4ee5\u63ed\u793a\u5fae\u751f\u7269\u591a\u6837\u6027\u7684\u79d8\u5bc6\uff0c\u7406\u89e3\u5b83\u4eec\u5728\u73af\u5883\u548c\u5bbf\u4e3b\u5065\u5eb7\u4e2d\u7684\u4f5c\u7528\u3002DirichletMultinomial\u5305\uff0c\u5c31\u662f\u6211\u4eec\u5728\u8fd9\u573a\u63a2\u9669\u4e2d\u7684\u795e\u5668\u3002\u5b83\u5229\u7528\u673a\u5668\u5b66\u4e60\u6784\u5efa\u4e86Dirichlet\u591a\u9879\u5f0f\u5206\u5e03\u6a21\u578b\u6765\u5206\u6790\u5fae\u751f\u7269\u7ec4\u6570\u636e\uff0c\u5e2e\u52a9\u6211\u4eec\u8bc6\u522b\u51fa\u5fae\u751f\u7269\u7fa4\u843d\u4e2d\u7684\u6a21\u5f0f\u548c\u8d8b\u52bf\u3002<\/p>\n\n\n\n<p>\u4f7f\u7528<a>DirichletMultinomial<\/a>\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u5904\u7406\u5927\u89c4\u6a21\u7684\u5fae\u751f\u7269\u7ec4\u6570\u636e\uff0c\u4ece\u800c\u9884\u6d4b\u5fae\u751f\u7269\u7684\u4e30\u5ea6\u5206\u5e03\uff0c\u63a2\u7d22\u5fae\u751f\u7269\u7fa4\u843d\u7684\u7ed3\u6784\u53d8\u5316\uff0c\u751a\u81f3\u662f\u5b83\u4eec\u5bf9\u73af\u5883\u53d8\u5316\u7684\u54cd\u5e94\u3002<strong>\u8bb0\u4f4f\uff0c\u8fd9\u4e2a\u5305\u9700\u8981\u8f83\u5927\u7684\u8ba1\u7b97\u8d44\u6e90\uff0c\u56e0\u6b64\u5efa\u8bae\u5728\u670d\u52a1\u5668\u4e0a\u8fdb\u884c\u8ba1\u7b97\uff0c\u5c0f\u679c\u8fd9\u91cc\u6709\u6027\u4ef7\u6bd4\u8d85\u9ad8\u7684\u670d\u52a1\u5668\u63a8\u8350\u54e6~<\/strong><\/p>\n\n\n\n<p>\u73b0\u5728\uff0c\u8ba9\u5c0f\u679c\u5e26\u9886\u5927\u5bb6\u4e00\u6b65\u6b65\u6df1\u5165\u5fae\u751f\u7269\u7ec4\u6570\u636e\u7684\u5206\u6790\u8fc7\u7a0b\uff0c\u4ece\u6570\u636e\u51c6\u5907\u5230\u6df1\u5ea6\u89e3\u6790\uff0c\u6211\u4eec\u5c06\u4e00\u540c\u63a2\u7d22\u5fae\u751f\u7269\u591a\u6837\u6027\u7684\u5965\u79d8\u3002<strong>\u5728\u8fd9\u4e2a\u65c5\u7a0b\u4e2d\u9047\u5230\u4efb\u4f55\u95ee\u9898\uff0c\u90fd\u4e0d\u8981\u72b9\u8c6b\uff0c\u5c0f\u679c\u968f\u65f6\u5728\u8fd9\u91cc\u4e3a\u4f60\u63d0\u4f9b\u5e2e\u52a9~<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u5148\u5b89\u88c5\u5e76\u52a0\u8f7dDirichletMultinomial\u5305\uff0c\u6b64\u5916\u8fd8\u6709 lattice \u5305\uff08\u7528\u4e8e\u53ef\u89c6\u5316\uff09\u548c parallel \u5305\uff08\u7528\u4e8e\u5728\u4ea4\u53c9\u9a8c\u8bc1\u671f\u95f4\u4f7f\u7528\u591a\u4e2a\u6838\u5fc3\uff09\u3002<\/p>\n\n\n\n<p>if (!require(&#8220;BiocManager&#8221;, quietly = TRUE))<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;install.packages(&#8220;BiocManager&#8221;)<\/p>\n\n\n\n<p>BiocManager::install(&#8220;DirichletMultinomial&#8221;)<\/p>\n\n\n\n<p>library(DirichletMultinomial)<\/p>\n\n\n\n<p>library(lattice)<\/p>\n\n\n\n<p>library(xtable)<\/p>\n\n\n\n<p>library(parallel)<\/p>\n\n\n\n<p>\u63a5\u7740\uff0c\u6211\u4eec\u8fdb\u884c\u4e00\u4e9b\u57fa\u672c\u7684\u8bbe\u7f6e\uff0c\u4f8b\u5982\u5c06\u5728R\u4e2d\u8bbe\u7f6e\u8f93\u51fa\u5bbd\u5ea6\uff0c\u4fee\u6539\u6d6e\u70b9\u6570\u7684\u663e\u793a\u7cbe\u5ea6\uff0c\u5728\u53ef\u89c6\u5316\u65f6\u91c7\u7528`.qualitative`\u7b49\u7b49\u3002<\/p>\n\n\n\n<p>options(width=70, digits=2)<\/p>\n\n\n\n<p>full &lt;- FALSE<\/p>\n\n\n\n<p>.qualitative &lt;- DirichletMultinomial:::.qualitative<\/p>\n\n\n\n<p>dev.off &lt;- function(&#8230;) invisible(grDevices::dev.off(&#8230;))<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u8ba9\u6211\u4eec\u6b65\u5165\u6b63\u9898\uff0c\u5f00\u59cb\u6211\u4eec\u7684\u5fae\u751f\u7269\u7ec4\u6570\u636e\u5206\u6790\u4e4b\u65c5~ \u6574\u4e2a\u65c5\u7a0b\u53ef\u4ee5\u5206\u6210\u4e09\u6b65\uff1a\u6570\u636e\u3001\u805a\u7c7b\u548c\u751f\u6210\u5206\u7c7b\u5668\u3002<\/p>\n\n\n\n<ul>\n<li>\u6570\u636e<\/li>\n<\/ul>\n\n\n\n<p>\u7b2c\u4e00\u6b65\uff0c\u83b7\u53d6\u6570\u636e\u3002\u6211\u4eec\u53ef\u4ee5\u8bfb\u53d6DirichletMultinomial\u5305\u4e2d\u7684\u6570\u636e\u6587\u4ef6&#8217;Twins.csv&#8217;\uff0c\u7136\u540e\u5c06\u6570\u636e\u8f6c\u6362\u4e3a\u6837\u672c\u00d7\u7269\u79cd\u7684\u8ba1\u6570\u77e9\u9635\u3002\u6570\u636e\u5305\u542b\u4e86\u5173\u4e8e\u6837\u672c\u548c\u7269\u79cd\uff08\u5fae\u751f\u7269\uff09\u7684\u8ba1\u6570\u4fe1\u606f\uff0c\u8fd9\u4e9b\u8ba1\u6570\u6570\u636e\u901a\u5e38\u6765\u81ea\u4e8e\u5fae\u751f\u7269\u7ec4\u5b66\u7814\u7a76\u4e2d\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u7528\u4e8e\u5206\u6790\u4e0d\u540c\u6837\u672c\u4e2d\u5fae\u751f\u7269\u7684\u5b58\u5728\u548c\u4e30\u5ea6\u3002<\/p>\n\n\n\n<p>fl &lt;- system.file(package=&#8221;DirichletMultinomial&#8221;, &#8220;extdata&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#8220;Twins.csv&#8221;)<\/p>\n\n\n\n<p>count &lt;- t(as.matrix(read.csv(fl, row.names=1)))<\/p>\n\n\n\n<p>count[1:5, 1:3]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"416\" height=\"100\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266535471_E2F7F7B8-0744-421d-9774-47516B22A9C8.png?resize=416%2C100\" alt=\"\" class=\"wp-image-61514\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266535471_E2F7F7B8-0744-421d-9774-47516B22A9C8.png?w=416 416w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266535471_E2F7F7B8-0744-421d-9774-47516B22A9C8.png?resize=300%2C72 300w\" sizes=\"(max-width: 416px) 100vw, 416px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5728count\u7684\u8f93\u51fa\u91cc\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5217\u540d\u8868\u793a\u4e0d\u540c\u7684\u5fae\u751f\u7269\uff0c\u884c\u540d\u4ee3\u8868\u4e0d\u540c\u7684\u6837\u672c\uff0ccounts\u5219\u8868\u793a\u5404\u79cd\u5fae\u751f\u7269\u5728\u5404\u6837\u672c\u91cc\u7684\u8ba1\u6570\u3002<\/p>\n\n\n\n<p>\u63a5\u7740\uff0c\u6211\u4eec\u53ef\u4ee5\u751f\u6210\u4e00\u4e2a\u5c55\u793a\u5fae\u751f\u7269\u7ec4\u6570\u636e\u4e2d\u5404\u5fae\u751f\u7269\u76f8\u5bf9\u4e30\u5ea6\uff08\u7ecf\u8fc7\u5bf9\u6570\u8f6c\u6362\uff09\u7684\u5bc6\u5ea6\u56fe\u3002\u6a2a\u8f74\u8868\u793a\u4e86\u5fae\u751f\u7269\u7684\u8868\u793a\u91cf\uff08\u4ee5log10\u8ba1\u6570\u8868\u793a\uff09\uff0c\u7eb5\u8f74\u8868\u793a\u4e86\u5bc6\u5ea6\u3002\u8fd9\u79cd\u56fe\u5f62\u6709\u52a9\u4e8e\u6211\u4eec\u7406\u89e3\u6570\u636e\u7684\u6574\u4f53\u5206\u5e03\uff0c\u7279\u522b\u662f\u5728\u5bf9\u6570\u5c3a\u5ea6\u4e0a\uff0c\u53ef\u4ee5\u66f4\u6e05\u6670\u5730\u770b\u5230\u54ea\u4e9b\u5fae\u751f\u7269\u7684\u4e30\u5ea6\u8f83\u9ad8\u6216\u8f83\u4f4e\uff0c\u4ee5\u53ca\u4e30\u5ea6\u5206\u5e03\u7684\u5f62\u72b6\uff08\u5982\u662f\u5426\u5448\u73b0\u6b63\u6001\u5206\u5e03\u3001\u662f\u5426\u6709\u957f\u5c3e\u7b49\uff09\u3002<\/p>\n\n\n\n<p>cnts &lt;- log10(colSums(count))<\/p>\n\n\n\n<p>pdf(&#8220;taxon-counts.pdf&#8221;)<\/p>\n\n\n\n<p>densityplot(cnts, xlim=range(cnts),<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xlab=&#8221;Taxon representation (log 10 count)&#8221;)<\/p>\n\n\n\n<p>dev.off()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"315\" height=\"312\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266554742_69851F60-362C-4824-97C8-CB3C55BFC6D9.png?resize=315%2C312\" alt=\"\" class=\"wp-image-61515\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266554742_69851F60-362C-4824-97C8-CB3C55BFC6D9.png?w=315 315w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266554742_69851F60-362C-4824-97C8-CB3C55BFC6D9.png?resize=300%2C297 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266554742_69851F60-362C-4824-97C8-CB3C55BFC6D9.png?resize=150%2C150 150w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266554742_69851F60-362C-4824-97C8-CB3C55BFC6D9.png?resize=100%2C100 100w\" sizes=\"(max-width: 315px) 100vw, 315px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<ul>\n<li>\u805a\u7c7b<\/li>\n<\/ul>\n\n\n\n<p>\u7b2c\u4e8c\u6b65\uff0c\u6211\u4eec\u53ef\u4ee5\u5f00\u59cb\u805a\u7c7b\u3002`dmn`\u51fd\u6570\u53ef\u4ee5\u7528\u4e8e\u62df\u5408Dirichlet-Multinomial\u6a21\u578b\uff0c\u5b83\u7684\u8f93\u5165\u662fcounts\u6570\u636e\u548c\u53c2\u6570k\uff08\u4ee3\u8868\u8981\u5efa\u6a21\u7684Dirichlet\u6210\u5206\u6570\u91cf\uff09\u3002\u6211\u4eec\u53ef\u4ee5\u9009\u53d6\u4e0d\u540c\u7684k\u503c\uff081~7\uff09\u8fdb\u884c\u62df\u5408\uff081~7\uff09\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u53ea\u5c55\u793ak=4\u7684\u7ed3\u679c\u3002<\/p>\n\n\n\n<p>if (full) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;fit &lt;- mclapply(1:7, dmn, count=count, verbose=TRUE)<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;save(fit, file=file.path(tempdir(), &#8220;fit.rda&#8221;))<\/p>\n\n\n\n<p>} else data(fit)<\/p>\n\n\n\n<p>fit[[4]]<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"294\" height=\"74\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266566322_5A9E62C6-519D-46eb-9BC6-195235A17D2D.png?resize=294%2C74\" alt=\"\" class=\"wp-image-61516\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u5728k=4\u7684\u7ed3\u679c\u8f93\u51fa\u4e2d\uff0cLaplace: 38781\uff0cBIC: 40425\uff0cAIC: 39477 \u5206\u522b\u662f\u8be5\u6a21\u578b\u7684\u62c9\u666e\u62c9\u65af\u8fd1\u4f3c\u503c\u3001\u8d1d\u53f6\u65af\u4fe1\u606f\u51c6\u5219\uff08BIC\uff09\u548c \u8d64\u6c60\u4fe1\u606f\u51c6\u5219\uff08AIC\uff09\uff0c\u53ef\u4ee5\u4f5c\u4e3a\u6a21\u578b\u9009\u62e9\u7684\u8bc4\u4ef7\u6307\u6807\u3002<\/p>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u7ed8\u5236\u4e0d\u540c Dirichlet \u6210\u5206\u6570\u91cf\u4e0b\u6a21\u578b\u62df\u5408\u5ea6\u7684\u6298\u7ebf\u56fe\uff0c\u5206\u6790\u56fe\u6211\u4eec\u53ef\u4ee5\u53d1\u73b0\u6700\u4f73\u62df\u5408\u662fk = 4 \u4e2a\u4e0d\u540c\u7684\u72c4\u5229\u514b\u96f7\u6210\u5206\u3002<\/p>\n\n\n\n<p>lplc &lt;- sapply(fit, laplace)<\/p>\n\n\n\n<p>pdf(&#8220;min-laplace.pdf&#8221;)<\/p>\n\n\n\n<p>plot(lplc, type=&#8221;b&#8221;, xlab=&#8221;Number of Dirichlet Components&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;ylab=&#8221;Model Fit&#8221;)<\/p>\n\n\n\n<p>dev.off()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"375\" height=\"346\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266575621_320BBDF4-FDB8-4fb7-8134-515384600B7C.png?resize=375%2C346\" alt=\"\" class=\"wp-image-61517\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266575621_320BBDF4-FDB8-4fb7-8134-515384600B7C.png?w=375 375w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266575621_320BBDF4-FDB8-4fb7-8134-515384600B7C.png?resize=300%2C277 300w\" sizes=\"(max-width: 375px) 100vw, 375px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u63a5\u7740\uff0c\u6211\u4eec\u53ef\u4ee5\u4ece\u4e2d\u9009\u62e9\u51fa\u62df\u5408\u6548\u679c\u6700\u4f73\u7684\u6a21\u578b\u5b58\u50a8\u5728&nbsp;best&nbsp;\u53d8\u91cf\u4e2d\u3002\u7136\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4ecebest\u5bf9\u8c61\u4e2d\u63d0\u53d6\u7279\u5b9a\u7684\u4fe1\u606f\u3002mixturewt \u51fd\u6570\u62a5\u544a\u62df\u5408\u6a21\u578b\u7684\u6743\u91cd pi \u548c\u540c\u8d28\u6027 theta\uff08\u503c\u8d8a\u5927\u8d8a\u540c\u8d28\uff09\u3002mixture \u8fd4\u56de\u6837\u672c x \u4f30\u8ba1\u7684\u72c4\u5229\u514b\u96f7\u6210\u5206\u7684\u77e9\u9635\uff1b\u53c2\u6570assign \u8fd4\u56de\u4e00\u4e2a\u957f\u5ea6\u7b49\u4e8e\u6837\u672c\u6570\u91cf\u7684\u5411\u91cf\uff0c\u8868\u793a\u5177\u6709\u6700\u5927\u503c\u7684\u6210\u5206\u3002<\/p>\n\n\n\n<p>(best &lt;- fit[[which.min(lplc)]])<\/p>\n\n\n\n<p>mixturewt(best)<\/p>\n\n\n\n<p>head(mixture(best), 3)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"318\" height=\"158\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266587052_95BA42A3-8D68-405c-A489-A7960274FF16.png?resize=318%2C158\" alt=\"\" class=\"wp-image-61518\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266587052_95BA42A3-8D68-405c-A489-A7960274FF16.png?w=318 318w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266587052_95BA42A3-8D68-405c-A489-A7960274FF16.png?resize=300%2C149 300w\" sizes=\"(max-width: 318px) 100vw, 318px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>Fitted\u51fd\u6570\u53ef\u4ee5\u63cf\u8ff0\u6bcf\u4e2a\u5206\u7c7b\u7fa4\uff08\u4e0b\u56fe\u6bcf\u683c\u4e2d\u7684\u6bcf\u4e2a\u70b9\uff09\u5bf9\u72c4\u5229\u514b\u96f7\u6210\u5206\u7684\u8d21\u732e\uff1b\u56fe\u4e2d\u70b9\u7684\u5bf9\u89d2\u7ebf\u8868\u660e\u72c4\u5229\u514b\u96f7\u6210\u5206\u662f\u5177\u6709\u76f8\u5173\u6027\u7684\uff0c\u53ef\u80fd\u53cd\u6620\u4e86\u6574\u4f53\u7684\u6570\u503c\u4e30\u5ea6\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"342\" height=\"350\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266595751_42D4EA79-AF2C-4e94-BE9A-68386E1FA896.png?resize=342%2C350\" alt=\"\" class=\"wp-image-61519\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266595751_42D4EA79-AF2C-4e94-BE9A-68386E1FA896.png?w=342 342w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266595751_42D4EA79-AF2C-4e94-BE9A-68386E1FA896.png?resize=293%2C300 293w\" sizes=\"(max-width: 342px) 100vw, 342px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u8ba1\u7b97\u6700\u4f73\u548c\u5355\u6210\u5206\u72c4\u5229\u514b\u96f7\u591a\u9879\u5f0f\u6a21\u578b\u4e4b\u95f4\u7684\u540e\u9a8c\u5747\u503c\u5dee\u5f02\uff0c\u5b83\u53ef\u4ee5\u8861\u91cf\u6bcf\u4e2a\u6210\u5206\u4e0e\u603b\u4f53\u5e73\u5747\u503c\u7684\u5dee\u5f02\uff1b\u800c\u603b\u548c\u5219\u662f\u4e0e\u5e73\u5747\u503c\u7684\u603b\u5dee\u5f02\u7684\u8861\u91cf\u6807\u51c6\u3002<\/p>\n\n\n\n<p>p0 &lt;- fitted(fit[[1]], scale=TRUE) &nbsp;&nbsp;&nbsp;&nbsp;# scale by theta<\/p>\n\n\n\n<p>p4 &lt;- fitted(best, scale=TRUE)<\/p>\n\n\n\n<p>colnames(p4) &lt;- paste(&#8220;m&#8221;, 1:4, sep=&#8221;&#8221;)<\/p>\n\n\n\n<p>(meandiff &lt;- colSums(abs(p4 &#8211; as.vector(p0))))<\/p>\n\n\n\n<p>sum(meandiff)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"356\" height=\"72\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266607593_25C53B40-352D-4db5-8FB9-C1162A699E5E.png?resize=356%2C72\" alt=\"\" class=\"wp-image-61520\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266607593_25C53B40-352D-4db5-8FB9-C1162A699E5E.png?w=356 356w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266607593_25C53B40-352D-4db5-8FB9-C1162A699E5E.png?resize=300%2C61 300w\" sizes=\"(max-width: 356px) 100vw, 356px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u8ba1\u7b97\u4e24\u4e2a\u62df\u5408\u6a21\u578b\u4e4b\u95f4\u6bcf\u884c\u7684\u7edd\u5bf9\u5dee\u5f02\u4e4b\u548c\uff0c\u5f97\u5230\u4e00\u4e2a\u5305\u542b\u5404\u79cd<a>\u5fae\u751f\u7269<\/a>\u7684\u5411\u91cf\u3002\u7ecf\u5904\u7406\u53ef\u4ee5\u5f97\u5230\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u62ec\u6bcf\u79cd\u5fae\u751f\u7269\u5728\u4e24\u4e2a\u6a21\u578b\u4e2d\u7684\u62df\u5408\u503c\u3001\u5dee\u5f02\u503c\u548c\u7d2f\u79ef\u5dee\u5f02\u6bd4\u7387\uff0c\u603b\u7ed3\u4e86\u5bf9\u6bcf\u4e2a\u72c4\u5229\u514b\u96f7\u6210\u5206\u7684\u5206\u7c7b\u8d21\u732e\u3002<\/p>\n\n\n\n<p>diff &lt;- rowSums(abs(p4 &#8211; as.vector(p0)))<\/p>\n\n\n\n<p>o &lt;- order(diff, decreasing=TRUE) &nbsp;#\u5bf9\u5dee\u5f02\u5411\u91cf\u8fdb\u884c\u964d\u5e8f\u6392\u5e8f<\/p>\n\n\n\n<p>cdiff &lt;- cumsum(diff[o]) \/ sum(diff) #\u8ba1\u7b97\u7d2f\u79ef\u5dee\u5f02\u6bd4\u7387\uff0c\u5373\u7d2f\u79ef\u5dee\u5f02\u4e4b\u548c\u9664\u4ee5\u603b\u5dee\u5f02\u4e4b\u548c<\/p>\n\n\n\n<p>df &lt;- head(cbind(Mean=p0[o], p4[o,], diff=diff[o], cdiff), 10)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"382\" height=\"204\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266626524_55B451DB-9F23-4b04-8580-202CF3F9CE3A.png?resize=382%2C204\" alt=\"\" class=\"wp-image-61521\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266626524_55B451DB-9F23-4b04-8580-202CF3F9CE3A.png?w=382 382w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266626524_55B451DB-9F23-4b04-8580-202CF3F9CE3A.png?resize=300%2C160 300w\" sizes=\"(max-width: 382px) 100vw, 382px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6211\u4eec\u4e5f\u53ef\u4ee5\u4f7f\u7528xtable\u51fd\u6570\u5c06\u6570\u636e\u6846df\u8f6c\u6362\u4e3a\u4e00\u4e2a\u683c\u5f0f\u5316\u7684\u8868\u683c\uff0c\u5e76\u8bbe\u7f6e\u8868\u683c\u7684\u6807\u9898\u3001\u6807\u7b7e\u3001\u5bf9\u9f50\u65b9\u5f0f\u7b49\u5c5e\u6027\u3002\u7136\u540e\u901a\u8fc7print\u51fd\u6570\u6253\u5370\u51fa\u8fd9\u4e2a\u8868\u683c\u3002<\/p>\n\n\n\n<p>xtbl &lt;- xtable(df,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;caption=&#8221;Taxonomic contributions (10 largest) to Dirichlet components.&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;label=&#8221;tab:meandiff&#8221;, align=&#8221;lccccccc&#8221;)<\/p>\n\n\n\n<p>print(xtbl, hline.after=0, caption.placement=&#8221;top&#8221;)<\/p>\n\n\n\n<p>\u4e0b\u56fe\u53ef\u4ee5\u5c55\u793a\u5fae\u751f\u7269\u6309\u7167\u72c4\u5229\u514b\u96f7\u6210\u5206\u6392\u5217\u7684\u60c5\u51b5\uff0c\u6bcf\u4e2a\u6837\u672c\u88ab\u653e\u5165\u5177\u6709\u6700\u5927\u62df\u5408\u503c\u7684\u6210\u5206\u4e2d\u3002\u901a\u8fc7\u4ee5\u4e0b\u4ee3\u7801\u5c06\u56fe\u8868\u4fdd\u5b58\u4e3a\u540d\u4e3a&#8221;heatmap1.pdf&#8221;\u7684PDF\u6587\u4ef6\uff1a<\/p>\n\n\n\n<p>pdf(&#8220;heatmap1.pdf&#8221;)<\/p>\n\n\n\n<p>heatmapdmn(count, fit[[1]], best, 30)<\/p>\n\n\n\n<p>dev.off()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"248\" height=\"243\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266636525_43D7DC95-3355-4941-8193-76B6490444AF.png?resize=248%2C243\" alt=\"\" class=\"wp-image-61522\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u5728\u56fe\u4e2d\uff0c\u7a84\u5217\u8868\u793a\u5fae\u751f\u7269\uff0c\u5bbd\u5217\u8868\u793a\u6210\u5206\u7684\u5e73\u5747\u503c\u3002\u6bcf\u884c\u5bf9\u5e94\u4e00\u4e2a\u5206\u7c7b\u7ec4\u3002\u989c\u8272\u7f16\u7801\u4ee3\u8868\u5e73\u65b9\u6839\u8ba1\u6570\uff0c\u6df1\u8272\u8868\u793a\u8f83\u5927\u7684\u8ba1\u6570\u3002\u8fd9\u5e45\u56fe\u53ef\u5e2e\u52a9\u89c2\u5bdf\u6837\u672c\u5728\u4e0d\u540c\u72c4\u5229\u514b\u96f7\u6210\u5206\u4e0b\u7684\u5206\u5e03\u60c5\u51b5\uff0c\u5e76\u5c55\u793a\u4e86\u8ba1\u6570\u503c\u7684\u76f8\u5bf9\u5927\u5c0f\u3002<\/p>\n\n\n\n<ul>\n<li>\u751f\u6210\u5206\u7c7b\u5668<\/li>\n<\/ul>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u4ee3\u7801\u8bfb\u53d6\u6bcf\u4e2a\u6837\u672c\u7684\u8868\u578b\u4fe1\u606f\uff0c\u5c06\u8868\u578b\u4fe1\u606f\u8fdb\u884c\u56e0\u5b50\u5316\u5904\u7406\uff08&#8217;Lean&#8217;\uff0c&#8217;Obese&#8217;\uff0c&#8217;Overweight&#8217;\uff09\uff0c\u518d\u5c06\u8868\u578b\u4fe1\u606f\u4e0e\u6570\u636e\u77e9\u9635\u4e2d\u7684\u884c\u540d\u79f0\u8fdb\u884c\u5339\u914d\uff0c\u5e76\u4f7f\u7528table(pheno)\u5bf9\u8868\u578b\u8fdb\u884c\u8ba1\u6570\uff0c\u5e76\u8f93\u51fa\u7ed3\u679c\u3002\u8f93\u51fa\u8868\u660e\u670961\u4e2a\u6837\u672c\u88ab\u5f52\u7c7b\u4e3a&#8217;Lean&#8217;\uff0c193\u4e2a\u6837\u672c\u4e3a&#8217;Obese&#8217;\uff0c24\u4e2a\u6837\u672c\u4e3a&#8217;Overwt&#8217;\u3002\u8fd9\u6709\u52a9\u4e8e\u4e86\u89e3\u6837\u672c\u4e2d\u4e0d\u540c\u8868\u578b\u7684\u5206\u5e03\u60c5\u51b5\u3002<\/p>\n\n\n\n<p>fl &lt;- system.file(package=&#8221;DirichletMultinomial&#8221;, &#8220;extdata&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&#8220;TwinStudy.t&#8221;)<\/p>\n\n\n\n<p>pheno0 &lt;- scan(fl)<\/p>\n\n\n\n<p>lvls &lt;- c(&#8220;Lean&#8221;, &#8220;Obese&#8221;, &#8220;Overwt&#8221;)<\/p>\n\n\n\n<p>pheno &lt;- factor(lvls[pheno0 + 1], levels=lvls)<\/p>\n\n\n\n<p>names(pheno) &lt;- rownames(count)<\/p>\n\n\n\n<p>table(pheno)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"180\" height=\"58\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266647243_A6111E15-CC66-4750-AC0E-8D360E319A28.png?resize=180%2C58\" alt=\"\" class=\"wp-image-61523\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u8fd9\u91cc\u6211\u4eec\u5c06\u6570\u636e\u6309\u8868\u578b\u5206\u6210\u5b50\u8ba1\u6570\uff0c\u6bcf\u4e2a\u8868\u578b\u4e00\u4e2a\u5b50\u8ba1\u6570\u3002\u6bcf\u4e2a\u5b50\u8ba1\u6570\u663e\u793a\u4e86\u5bf9\u5e94\u8868\u578b\u7684\u6837\u672c\u6570\u3002<\/p>\n\n\n\n<p>counts &lt;- lapply(levels(pheno), csubset, count, pheno)<\/p>\n\n\n\n<p>sapply(counts, dim)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"160\" height=\"59\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266659379_FEDB7C1D-23B7-48b9-8E23-C27F70EE2DD4.png?resize=160%2C59\" alt=\"\" class=\"wp-image-61524\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u63a5\u7740\uff0c\u9700\u8981\u5bf9\u8868\u578b\u4fe1\u606f\u8fdb\u884c\u76f8\u5e94\u66f4\u65b0\uff0c\u53ea\u4fdd\u7559&#8217;Lean&#8217;\u548c&#8217;Obese&#8217;\u4e24\u79cd\u8868\u578b\u3002<\/p>\n\n\n\n<p>keep &lt;- c(&#8220;Lean&#8221;, &#8220;Obese&#8221;)<\/p>\n\n\n\n<p>count &lt;- count[pheno %in% keep,]<\/p>\n\n\n\n<p>pheno &lt;- factor(pheno[pheno %in% keep], levels=keep)<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5e26\u5927\u5bb6\u4f7f\u7528\u4e00\u4e2a\u51fd\u6570\u2014\u2014dmngroup\u51fd\u6570\uff0c\u5b83\u7528\u4e8e\u4e3a\u6bcf\u4e2a\u7ec4\u8bc6\u522b\u6700\u4f73\uff08\u6700\u5c0fLaplace\u5f97\u5206\uff09\u7684Dirichletmultinomial\u6a21\u578b\u3002<\/p>\n\n\n\n<p>if (full) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;bestgrp &lt;- dmngroup(count, pheno, k=1:5, verbose=TRUE,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;mc.preschedule=FALSE)<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;save(bestgrp, file=file.path(tempdir(), &#8220;bestgrp.rda&#8221;))<\/p>\n\n\n\n<p>} else data(bestgrp)<\/p>\n\n\n\n<p>Lean\u7ec4\u7531\u4e00\u4e2a\u6210\u5206\u6a21\u578b\u63cf\u8ff0\uff0cObese\u7ec4\u7531\u4e00\u4e2a\u5305\u542b\u4e09\u4e2a\u6210\u5206\u7684\u6a21\u578b\u63cf\u8ff0\u3002\u539f\u59cb\u5355\u7ec4\uff08\u6700\u4f73\uff09\u6a21\u578b\u7684\u56db\u4e2aDirichle\u6210\u5206\u4e2d\uff0c\u4e09\u4e2a\u5728Obese\u7ec4\u4e2d\uff0c\u53e6\u4e00\u4e2a\u5728Lean\u7ec4\u4e2d\u3002\u4e24\u7ec4\u6a21\u578b\u7684\u603bLaplace\u5206\u6570\u6bd4\u5355\u7ec4\u6a21\u578b\u4f4e\uff0c\u8868\u660e\u4ece\u5355\u72ec\u8003\u8651\u7ec4\u522b\u65f6<a>\u83b7\u5f97\u4e86\u4fe1\u606f\u589e\u76ca<\/a>\u3002<\/p>\n\n\n\n<p>\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528bestgrp\u67e5\u770b\u6700\u4f73\u6a21\u578b\u7684\u6458\u8981\u4fe1\u606f\uff0c\u5305\u62ec\u6bcf\u4e2a\u7ec4\uff08Lean\u548cObese\uff09\u7684\u6837\u672c\u6570\u91cf\u3001\u7269\u79cd\u6570\u3001\u8d1f\u5bf9\u6570\u4f3c\u7136\uff08NLE\uff09\u3001\u5bf9\u6570\u884c\u5217\u5f0f\uff08LogDet\uff09\u3001Laplace\u5f97\u5206\u3001\u8d1d\u53f6\u65af\u4fe1\u606f\u51c6\u5219\uff08BIC\uff09\u548c\u8d64\u6c60\u4fe1\u606f\u51c6\u5219\uff08AIC\uff09\u7b49\u7edf\u8ba1\u91cf\u3002<\/p>\n\n\n\n<p>bestgrp<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"400\" height=\"87\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266671129_26FFF73A-52A4-49c9-A091-3DF0A78CED50.png?resize=400%2C87\" alt=\"\" class=\"wp-image-61525\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266671129_26FFF73A-52A4-49c9-A091-3DF0A78CED50.png?w=400 400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266671129_26FFF73A-52A4-49c9-A091-3DF0A78CED50.png?resize=300%2C65 300w\" sizes=\"(max-width: 400px) 100vw, 400px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5bf9bestgrp\u4e2d\u7684\u6bcf\u4e2a\u7ec4\uff08Lean\u548cObese\uff09\u5e94\u7528mixturewt\u51fd\u6570\uff0c\u53ef\u4ee5\u663e\u793a\u6bcf\u4e2a\u7ec4\u6a21\u578b\u7684\u6210\u5206\u6743\u91cd\uff08pi\uff09\u548c\u540c\u8d28\u6027\uff08theta\uff09\u3002<\/p>\n\n\n\n<p>lapply(bestgrp, mixturewt)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"208\" height=\"152\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266680907_D83949C8-4B6C-406b-AE14-A6115FBD9AC4.png?resize=208%2C152\" alt=\"\" class=\"wp-image-61526\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>\u6211\u4eec\u8fd8\u53ef\u4ee5\u8ba1\u7b97\u5404\u7ec4\uff08Lean\u548cObese\uff09\u3001\u6574\u4f53\u7ec4\u5408\uff08Lean+Obese\uff09\u4ee5\u53ca\u5355\u4e00\u7ec4\u6a21\u578b\u7684Laplace\u5206\u6570\uff0c\u7ed3\u679c\u8868\u660eLean\u7ec4\u548cObese\u7ec4\u7ec4\u5408\u6a21\u578b\u7684\u603bLaplace\u5206\u6570\u8f83\u4f4e\uff0c\u8fd9\u8868\u660e\u5355\u4e00\u7ec4\u6a21\u578b\u83b7\u5f97\u4e86\u4fe1\u606f\u589e\u76ca\u3002<\/p>\n\n\n\n<p>c(sapply(bestgrp, laplace),<\/p>\n\n\n\n<p>&nbsp;&nbsp;`Lean+Obese`=sum(sapply(bestgrp, laplace)),<\/p>\n\n\n\n<p>&nbsp;&nbsp;Single=laplace(best))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"350\" height=\"80\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266689169_6A08A08F-2F8D-4518-9C5D-B520E580D660.png?resize=350%2C80\" alt=\"\" class=\"wp-image-61527\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266689169_6A08A08F-2F8D-4518-9C5D-B520E580D660.png?w=350 350w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266689169_6A08A08F-2F8D-4518-9C5D-B520E580D660.png?resize=300%2C69 300w\" sizes=\"(max-width: 350px) 100vw, 350px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6700\u540e\uff0c\u6211\u4eec\u8981\u4f7f\u7528\u6a21\u578b\u8fdb\u884c\u9884\u6d4b\u5566\uff01\u4f7f\u7528predict\u51fd\u6570\u53ef\u4ee5\u5c06\u6837\u672c\u5206\u914d\u5230\u4e0d\u540c\u7684\u7c7b\u522b\u4e2d\u3002<\/p>\n\n\n\n<p>xtabs(~pheno + predict(bestgrp, count, assign=TRUE))<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"400\" height=\"74\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266703018_3DC66E9B-B37E-4232-90D5-1257938308D5.png?resize=400%2C74\" alt=\"\" class=\"wp-image-61528\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266703018_3DC66E9B-B37E-4232-90D5-1257938308D5.png?w=400 400w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266703018_3DC66E9B-B37E-4232-90D5-1257938308D5.png?resize=300%2C56 300w\" sizes=\"(max-width: 400px) 100vw, 400px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5728\u8f93\u51fa\u7684\u77e9\u9635\u4e2d\uff0c\u884c\u4ee3\u8868\u5b9e\u9645\u7c7b\u522b\uff0c\u5217\u4ee3\u8868\u9884\u6d4b\u7c7b\u522b\u3002\u8f93\u51fa\u503c\u8868\u793a\u6bcf\u4e2a\u7c7b\u522b\u7684\u6837\u672c\u6570\u3002\u5728\u77e9\u9635\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u5bf9\u4e8e\u5b9e\u9645\u4e3a&#8221;Lean&#8221;\u7684\u6837\u672c\uff0c\u670938\u4e2a\u88ab\u6b63\u786e\u5730\u9884\u6d4b\u4e3a&#8221;Lean&#8221;\uff0c23\u4e2a\u88ab\u9519\u8bef\u5730\u9884\u6d4b\u4e3a&#8221;Obese&#8221;\u3002\u5bf9\u4e8e\u5b9e\u9645\u4e3a&#8221;Obese&#8221;\u7684\u6837\u672c\uff0c\u6709178\u4e2a\u88ab\u6b63\u786e\u5730\u9884\u6d4b\u4e3a&#8221;Obese&#8221;\uff0c\u800c\u670915\u4e2a\u88ab\u9519\u8bef\u5730\u9884\u6d4b\u4e3a&#8221;Lean&#8221;<a>\u3002<\/a>\u663e\u7136\uff0c\u6a21\u578b\u5bf9\u4e8e&#8221;Obese&#8221;\u7684\u9884\u6d4b\u66f4\u52a0\u51c6\u786e\u3002<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528cvdmngroup \u51fd\u6570\u6267\u884c\u4ea4\u53c9\u9a8c\u8bc1\uff0c\u53ef\u4ee5\u6839\u636e\u5206\u7ec4\u60c5\u51b5\u8fdb\u884cleave-one-out\uff08LOO\uff09\u4ea4\u53c9\u9a8c\u8bc1\u3002\u6ce8\u610f\u54e6\uff0c\u8fd9\u662f\u4e00\u4e2a\u8ba1\u7b97\u91cf\u5f88\u5927\u7684\u6b65\u9aa4\uff0c\u53ef\u80fd\u9700\u8981\u4e00\u70b9\u65f6\u95f4\u3002<\/p>\n\n\n\n<p>if (full) {<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;## full leave-one-out; expensive!<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;xval &lt;- cvdmngroup(nrow(count), count, c(Lean=1, Obese=3), pheno,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;verbose=TRUE, mc.preschedule=FALSE)<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;save(xval, file=file.path(tempdir(), &#8220;xval.rda&#8221;))<\/p>\n\n\n\n<p>} else data(xval)<\/p>\n\n\n\n<p>\u6700\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u8868\u578b\u548c\u9884\u6d4b\u7ed3\u679c\u5206\u522b\u751f\u6210\u9488\u5bf9\u5355\u7ec4\/\u4e24\u7ec4\/\u6574\u5408\u5206\u7c7b\u5668\u7684ROC\u66f2\u7ebf\u3002<\/p>\n\n\n\n<p>bst &lt;- roc(pheno[rownames(count)] == &#8220;Obese&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;predict(bestgrp, count)[,&#8221;Obese&#8221;])<\/p>\n\n\n\n<p>bst$Label &lt;- &#8220;Single&#8221;<\/p>\n\n\n\n<p>two &lt;- roc(pheno[rownames(xval)] == &#8220;Obese&#8221;,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xval[,&#8221;Obese&#8221;])<\/p>\n\n\n\n<p>two$Label &lt;- &#8220;Two group&#8221;<\/p>\n\n\n\n<p>both &lt;- rbind(bst, two)<\/p>\n\n\n\n<p>pars &lt;- list(superpose.line=list(col=.qualitative[1:2], lwd=2))<\/p>\n\n\n\n<p>pdf(&#8220;roc.pdf&#8221;)<\/p>\n\n\n\n<p>xyplot(TruePostive ~ FalsePositive, group=Label, both,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;type=&#8221;l&#8221;, par.settings=pars,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;auto.key=list(lines=TRUE, points=FALSE, x=.6, y=.1),<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;xlab=&#8221;False Positive&#8221;, ylab=&#8221;True Positive&#8221;)<\/p>\n\n\n\n<p>dev.off()<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"324\" height=\"315\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266720771_D2774327-2543-42b5-975B-15CFF50BE994.png?resize=324%2C315\" alt=\"\" class=\"wp-image-61529\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266720771_D2774327-2543-42b5-975B-15CFF50BE994.png?w=324 324w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730266720771_D2774327-2543-42b5-975B-15CFF50BE994.png?resize=300%2C292 300w\" sizes=\"(max-width: 324px) 100vw, 324px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u4e0a\u56fe\u663e\u793a\u7684ROC\u66f2\u7ebf\u56fe\uff0c\u5c55\u793a\u4e86\u5355\u7ec4\u5206\u7c7b\u5668\u548c\u4e24\u7ec4\u5206\u7c7b\u5668\u7684\u6027\u80fd\u5bf9\u6bd4\u3002\u5176\u4e2d\uff0c\u6a2a\u8f74\u4e3aFalse Positive\uff0c\u7eb5\u8f74\u4e3aTrue Positive\u3002\u901a\u8fc7ROC\u66f2\u7ebf\u5bf9\u5355\u7ec4\u548c\u4e24\u7ec4\u5206\u7c7b\u5668\u7684\u6027\u80fd\u8fdb\u884c\u4e86\u6bd4\u8f83\uff0c\u7ed3\u679c\u663e\u793a\u5355\u7ec4\u5206\u7c7b\u5668\u7684\u8868\u73b0\u4f18\u4e8e\u4e24\u7ec4\u5206\u7c7b\u5668\u3002<\/p>\n\n\n\n<p>\u600e\u4e48\u6837\uff0cAI\u7684\u4e16\u754c\u662f\u4e0d\u662f\u5f88\u795e\u5947\uff1f\u597d\u5566\uff0c\u5c0f\u679c\u5df2\u7ecf\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b8c\u6210\u4e86<a><\/a>DirichletMultinomial\u5305\u7684\u521d\u6b65\u63a2\u7d22\uff0c\u4f60\u6709\u6ca1\u6709\u5bf9AI\u5728\u5206\u6790\u5fae\u751f\u7269\u7ec4\u6570\u636e\u4e0a\u7684\u5e94\u7528\u6709\u4e86\u611f\u6027\u7684\u8ba4\u8bc6\u5462\uff1f\u73b0\u5728\uff0c\u4f60\u53ef\u4ee5\u5f00\u59cb\u81ea\u5df1\u52a8\u624b\uff0c\u5229\u7528DirichletMultinomial\u5305\u6765\u6784\u5efa\u5c5e\u4e8e\u4f60\u81ea\u5df1\u7684\u6a21\u578b\u5566\uff01<\/p>\n\n\n\n<p>\u65e0\u8bba\u4f60\u662f\u5728\u4f18\u5316\u4ee3\u7801\uff0c\u8fd8\u662f\u5728\u4e91\u7aef\u8fdb\u884c\u4fbf\u6377\u7684\u5206\u6790\uff0c\u4e91\u751f\u4fe1\u795e\u5668\u90fd\u80fd\u4e3a\u4f60\u63d0\u4f9b\u5f3a\u5927\u7684\u652f\u6301\u3002<strong>\u6b22\u8fce<\/strong><strong>\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u795e\u5668<\/strong><strong>\uff0c<\/strong><strong>\u53ea\u9700<\/strong><strong>\u4e00\u952e<\/strong><strong>\u4e0a\u4f20\u6570\u636e\uff0c\u60f3\u8981\u7684\u56fe\u5c31\u80fd\u8f7b\u677e<\/strong><strong>get~<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/strong><a href=\"http:\/\/www.biocloudservice.com\/home.html\"><strong>http:\/\/www.biocloudservice.com\/home.html<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u55e8\uff0c\u63a2\u7d22\u8005\u4eec\uff0c\u5c0f\u679c\u5411\u5bfc\u518d\u6b21\u6b22\u8fce\u4f60\u4eec\uff01\u4eca\u5929\uff0c\u6211\u4eec\u7684\u63a2\u9669\u76ee\u7684\u5730\u662f\u795e\u79d8\u800c\u53c8\u590d\u6742\u7684\u5fae\u751f\u7269\u7ec4\u4e16\u754c\u3002\u5728\u8fd9\u4e2a\u4e16\u754c\u91cc\uff0c\u6bcf\u4e00\u4e2a\u5fae [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/61513"}],"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=61513"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61513\/revisions"}],"predecessor-version":[{"id":61530,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61513\/revisions\/61530"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61513"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61513"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61513"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}