{"id":54820,"date":"2024-06-16T14:29:32","date_gmt":"2024-06-16T06:29:32","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54820"},"modified":"2024-06-16T14:29:32","modified_gmt":"2024-06-16T06:29:32","slug":"%e4%bd%bf%e7%94%a8r%e8%af%ad%e8%a8%80%e5%8c%85genefilter%e9%a2%84%e5%a4%84%e7%90%86%e6%95%b0%e6%8d%ae%e5%92%8c%e7%ad%9b%e9%80%89%e6%95%b0%e6%8d%ae%e7%9a%84%e4%bf%9d%e5%a7%86%e7%ba%a7%e6%95%99%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54820","title":{"rendered":"\u4f7f\u7528R\u8bed\u8a00\u5305genefilter\u9884\u5904\u7406\u6570\u636e\u548c\u7b5b\u9009\u6570\u636e\u7684\u4fdd\u59c6\u7ea7\u6559\u7a0b"},"content":{"rendered":"


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powered-by=\"xiumi.us\">\n<section>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u5728\u751f\u7269\u5b66\u7814\u7a76\u4e2d\uff0c\u6211\u4eec\u7ecf\u5e38\u9700\u8981\u5904\u7406\u5927\u89c4\u6a21\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u8fd9\u4e9b\u6570\u636e\u53ef\u80fd\u6765\u81ea\u4e0d\u540c\u6761\u4ef6\u4e0b\u7684\u5b9e\u9a8c\u6216\u75be\u75c5\u6837\u672c\u3002<\/span><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">genefilter\u63d0\u4f9b\u4e86\u4e00\u5957\u529f\u80fd\u5f3a\u5927\u7684\u5de5\u5177\uff0c\u7528\u4e8e\u5904\u7406\u8fd9\u4e9b\u590d\u6742\u7684\u6570\u636e\uff0c\u5e76\u4ece\u4e2d\u8bc6\u522b\u51fa\u4e0e\u7814\u7a76\u95ee\u9898\u76f8\u5173\u7684\u57fa\u56e0\u3002<\/span><br 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code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">> install.packages(\"genefilter\")<\/span><\/code><code><span class=\"code-snippet_outer\">> library(genefilter)<\/span><\/code><\/pre>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, 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style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u793a\u4f8b\uff1a<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u5f53\u4f7f\u7528R\u4e2d\u7684genefilter\u5305\u8fdb\u884c\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u9884\u5904\u7406\u65f6\uff0c\u6211\u4eec\u901a\u5e38\u4f1a\u6d89\u53ca\u6570\u636e\u7684\u8bfb\u53d6\u3001\u6570\u636e\u6e05\u6d17\u3001\u5f52\u4e00\u5316\u548c\u53ef\u89c6\u5316\u3002\u4e0b\u9762\u662f\u4e00\u4e2a\u7b80\u5355\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u9884\u5904\u7406\u793a\u4f8b\uff0c\u4f7f\u7528R\u4e2d\u81ea\u5e26\u7684iris\u6570\u636e\u96c6\u3002<\/span><span style=\"mso-spacerun:'yes';font-family:\u5b8b\u4f53;mso-ascii-font-family:Calibri;mso-hansi-font-family:Calibri;mso-bidi-font-family:'Times New Roman';\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1080\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-02_\u4f7f\u7528R\u8bed\u8a00\u5305genefilter\u9884\u5904\u7406\u6570\u636e\u548c\u7b5b\u9009\u6570\u636e\u7684\u4fdd\u59c6\u7ea7\u6559\u7a0b\/1_IlmBAWe69EMUPMhNEgrv6NXX85lJxg.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgibzL8qUpQROfe8ebc3gNSnu1dIlmBAWe69EMUPMhNEgrv6NXX85lJxg\/640?wx_fmt=jpeg'\" \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><\/span><\/p>\n<p><span style=\"white-space:pre-wrap;font-family: Consolas, "Liberation Mono", Menlo, Courier, monospace;font-size: 14px;background-color: rgb(250, 250, 250);color: rgb(51, 51, 51);letter-spacing: 0.034em;\">\u200d<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"># \u5b89\u88c5\u548c\u52a0\u8f7d\u6240\u9700\u7684\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">> install.packages(\"genefilter\")<\/span><\/code><code><span class=\"code-snippet_outer\">> install.packages(\"Biobase\") # \u5982\u679c\u672a\u5b89\u88c5Biobase\u5305\u7684\u8bdd<\/span><\/code><code><span class=\"code-snippet_outer\">> library(genefilter)<\/span><\/code><code><span class=\"code-snippet_outer\">> library(Biobase)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u4f7f\u7528iris\u6570\u636e\u96c6\u4f5c\u4e3a\u793a\u4f8b\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">> data(iris)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u5c06iris\u6570\u636e\u96c6\u7684\u524d\u56db\u5217\u4f5c\u4e3a\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff08\u793a\u4f8b\u4e2d\u5e76\u4e0d\u662f\u771f\u5b9e\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff09<\/span><\/code><code><span class=\"code-snippet_outer\">> gene_expr <- iris[, 1:4]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u67e5\u770b\u539f\u59cb\u6570\u636e\u7684\u524d\u51e0\u884c<\/span><\/code><code><span class=\"code-snippet_outer\">> head(gene_expr)<\/span><\/code><code><span class=\"code-snippet_outer\"> Sepal.Length Sepal.Width Petal.Length Petal.Width<\/span><\/code><code><span class=\"code-snippet_outer\">1 5.1 3.5 1.4 0.2<\/span><\/code><code><span class=\"code-snippet_outer\">2 4.9 3.0 1.4 0.2<\/span><\/code><code><span class=\"code-snippet_outer\">3 4.7 3.2 1.3 0.2<\/span><\/code><code><span class=\"code-snippet_outer\">4 4.6 3.1 1.5 0.2<\/span><\/code><code><span class=\"code-snippet_outer\">5 5.0 3.6 1.4 0.2<\/span><\/code><code><span class=\"code-snippet_outer\">6 5.4 3.9 1.7 0.4<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u5f52\u4e00\u5316<\/span><\/code><code><span class=\"code-snippet_outer\"># \u5728\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\uff0c\u5f52\u4e00\u5316\u662f\u4e3a\u4e86\u4f7f\u4e0d\u540c\u57fa\u56e0\u7684\u8868\u8fbe\u503c\u5728\u6570\u91cf\u7ea7\u4e0a\u4fdd\u6301\u4e00\u81f4\uff0c\u4fbf\u4e8e\u6bd4\u8f83\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">> normalized_data <- scale(gene_expr)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u67e5\u770b\u5f52\u4e00\u5316\u540e\u7684\u6570\u636e\u524d\u51e0\u884c<\/span><\/code><code><span class=\"code-snippet_outer\">> head(normalized_data)<\/span><\/code><code><span class=\"code-snippet_outer\"> Sepal.Length Sepal.Width Petal.Length Petal.Width<\/span><\/code><code><span class=\"code-snippet_outer\">[1,] -0.8976739 1.01560199 -1.335752 -1.311052<\/span><\/code><code><span class=\"code-snippet_outer\">[2,] -1.1392005 -0.13153881 -1.335752 -1.311052<\/span><\/code><code><span class=\"code-snippet_outer\">[3,] -1.3807271 0.32731751 -1.392399 -1.311052<\/span><\/code><code><span class=\"code-snippet_outer\">[4,] -1.5014904 0.09788935 -1.279104 -1.311052<\/span><\/code><code><span class=\"code-snippet_outer\">[5,] -1.0184372 1.24503015 -1.335752 -1.311052<\/span><\/code><code><span class=\"code-snippet_outer\">[6,] -0.5353840 1.93331463 -1.165809 -1.048667<\/span><\/code><code><span class=\"code-snippet_outer\"># Boxplot<\/span><\/code><code><span class=\"code-snippet_outer\">> boxplot(normalized_data, col = \"lightblue\", main = \"Normalized Gene Expression\",<\/span><\/code><code><span class=\"code-snippet_outer\">+ xlab = \"Gene\", ylab = \"Normalized Expression\")<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.8605042016806723\" data-s=\"300,640\" data-type=\"png\" data-w=\"595\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_j2ibtKjqqwe2ForGt7AjNnWKQFMorQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQia8uibCFvD1HPG3k96tCkTXKyysj2ibtKjqqwe2ForGt7AjNnWKQFMorQ\/640?wx_fmt=png'\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">> install.packages(\"genefilter\")<\/span><\/code><code><span class=\"code-snippet_outer\">> library(genefilter)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.860062893081761\" data-s=\"300,640\" data-type=\"png\" data-w=\"636\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-02_\u4f7f\u7528R\u8bed\u8a00\u5305genefilter\u9884\u5904\u7406\u6570\u636e\u548c\u7b5b\u9009\u6570\u636e\u7684\u4fdd\u59c6\u7ea7\u6559\u7a0b\/3_VpF8al0ibNL1qlcGTTzFiapYial74w.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQNEKYmXIBRSeL6y45OG9fvQricwFRVpF8al0ibNL1qlcGTTzFiapYial74w\/640?wx_fmt=png'\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"># \u5229\u7528\u53ef\u89c6\u5316\u56fe\u8868\uff0c\u6211\u4eec\u53ef\u4ee5\u521d\u6b65\u89c2\u5bdf\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u7684\u5206\u5e03\u60c5\u51b5\u548c\u57fa\u56e0\u4e4b\u95f4\u7684\u76f8\u5173\u6027\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"># \u7136\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u7814\u7a76\u95ee\u9898\u548c\u9700\u8981\uff0c\u8fdb\u4e00\u6b65\u4f7f\u7528genefilter\u5305\u63d0\u4f9b\u7684\u529f\u80fd\uff0c\u7b5b\u9009\u51fa\u611f\u5174\u8da3\u7684\u57fa\u56e0\u5e76\u8fdb\u884c\u6df1\u5165\u5206\u6790\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">\u9664\u4e86\u6570\u636e\u9884\u5904\u7406\u5916\uff0cgenefilter\u8fd8\u63d0\u4f9b\u4e86\u4e30\u5bcc\u7684\u7b5b\u9009\u65b9\u6cd5\uff0c\u7528\u4e8e\u4ece\u5927\u89c4\u6a21\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\u6311\u9009\u51fa\u4e0e\u7814\u7a76\u95ee\u9898\u6700\u76f8\u5173\u7684\u57fa\u56e0\u3002\u8fd9\u4e9b\u7b5b\u9009\u65b9\u6cd5\u53ef\u4ee5\u6839\u636e\u57fa\u56e0\u7684\u8868\u8fbe\u6a21\u5f0f\u3001\u53d8\u5f02\u7a0b\u5ea6\u3001\u76f8\u5173\u6027\u7b49\u6307\u6807\u8fdb\u884c\u7b5b\u9009\uff0c\u5e76\u4e14\u53ef\u4ee5\u6839\u636e\u7528\u6237\u7684\u9700\u6c42\u8fdb\u884c\u5b9a\u5236\u3002\u901a\u8fc7\u8fd9\u4e9b\u7b5b\u9009\u65b9\u6cd5\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u5feb\u901f\u5730\u4ece\u6d77\u91cf\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\u627e\u5230\u90a3\u4e9b\u5bf9\u4e8e\u7814\u7a76\u95ee\u9898\u6700\u6709\u610f\u4e49\u7684\u57fa\u56e0\uff0c\u4ece\u800c\u7f29\u5c0f\u7814\u7a76\u8303\u56f4\uff0c\u63d0\u9ad8\u7814\u7a76\u6548\u7387\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">\u793a\u4f8b\uff1a<\/span><\/code><code><span class=\"code-snippet_outer\">airway\u6570\u636e\u96c6\u5305\u542b\u4e86\u6765\u81ea\u4eba\u7c7b\u6c14\u9053\u4e0a\u76ae\u7ec6\u80de\u7684RNA-seq\u6570\u636e\uff0c\u7528\u4e8e\u7814\u7a76\u54ee\u5598\u75c5\u7684\u57fa\u56e0\u8868\u8fbe\u53d8\u5316\u3002\u6211\u4eec\u5c06\u4f7f\u7528genefilter\u5305\u4e2d\u7684\u7b5b\u9009\u65b9\u6cd5\u6765\u6839\u636e\u57fa\u56e0\u7684\u8868\u8fbe\u6a21\u5f0f\u548c\u53d8\u5f02\u7a0b\u5ea6\u8fdb\u884c\u7b5b\u9009\uff0c\u5e76\u901a\u8fc7\u53ef\u89c6\u5316\u56fe\u8868\u6765\u5c55\u793a\u7ed3\u679c\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u5b89\u88c5\u548c\u52a0\u8f7d\u6240\u9700\u7684\u5305<\/span><\/code><code><span class=\"code-snippet_outer\">> install.packages(\"genefilter\")<\/span><\/code><code><span class=\"code-snippet_outer\">> install.packages(\"airway\") # \u5982\u679c\u672a\u5b89\u88c5airway\u5305\u7684\u8bdd<\/span><\/code><code><span class=\"code-snippet_outer\">> library(genefilter)<\/span><\/code><code><span class=\"code-snippet_outer\">> library(airway)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u52a0\u8f7dairway\u6570\u636e\u96c6<\/span><\/code><code><span class=\"code-snippet_outer\">> data(airway)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u63d0\u53d6\u57fa\u56e0\u8868\u8fbe\u6570\u636e\uff0c\u5047\u8bbe\u6570\u636e\u662f\u77e9\u9635\u5f62\u5f0f\uff0c\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c<\/span><\/code><code><span class=\"code-snippet_outer\">> gene_expr <- assay(airway)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u67e5\u770b\u539f\u59cb\u6570\u636e\u7684\u524d\u51e0\u884c<\/span><\/code><code><span class=\"code-snippet_outer\">> head(gene_expr)<\/span><\/code><code><span class=\"code-snippet_outer\"> SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516 SRR1039517 SRR1039520 SRR1039521<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000003 679 448 873 408 1138 1047 770 572<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000005 0 0 0 0 0 0 0 0<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000419 467 515 621 365 587 799 417 508<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000457 260 211 263 164 245 331 233 229<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000460 60 55 40 35 78 63 76 60<\/span><\/code><code><span class=\"code-snippet_outer\">ENSG00000000938 0 0 2 0 1 0 0 0<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u7b5b\u9009\u65b9\u6cd5\u4e00\uff1a\u6839\u636e\u57fa\u56e0\u7684\u8868\u8fbe\u6a21\u5f0f\u8fdb\u884c\u7b5b\u9009<\/span><\/code><code><span class=\"code-snippet_outer\"># \u4f7f\u7528genefilter\u5305\u4e2d\u7684`rowSds`\u51fd\u6570\u8ba1\u7b97\u6bcf\u4e2a\u57fa\u56e0\u7684\u6807\u51c6\u5dee\uff08\u8868\u8fbe\u6a21\u5f0f\uff09\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"># \u7136\u540e\u9009\u62e9\u6807\u51c6\u5dee\u5927\u4e8e\u6307\u5b9a\u9608\u503c\u7684\u57fa\u56e0\u4f5c\u4e3a\u7b5b\u9009\u7ed3\u679c\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">> threshold_sd <- 1 # \u8bbe\u7f6e\u6807\u51c6\u5dee\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">> selected_genes_by_sd <- gene_expr[rowSds(gene_expr) > threshold_sd, ]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u53ef\u89c6\u5316\uff1a\u7bb1\u7ebf\u56fe\u6bd4\u8f83\u7b5b\u9009\u524d\u540e\u7684\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">> par(mfrow = c(1, 2))<\/span><\/code><code><span class=\"code-snippet_outer\">> boxplot(gene_expr, col = \"lightblue\", main = \"Before Filtering\", xlab = \"Gene\", ylab = \"Expression\")<\/span><\/code><code><span class=\"code-snippet_outer\">> boxplot(selected_genes_by_sd, col = \"lightgreen\", main = \"After Filtering by SD\", xlab = \"Gene\", ylab = \"Expression\")<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.8598265895953757\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_1VZiaCBNlsbIA1uSicmjr3xDLYNxKA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQyb2iayuUPYIO52SnnLgnaUVmnmP1VZiaCBNlsbIA1uSicmjr3xDLYNxKA\/640?wx_fmt=png'\" \/><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"># \u7b5b\u9009\u65b9\u6cd5\u4e8c\uff1a\u6839\u636e\u57fa\u56e0\u7684\u53d8\u5f02\u7a0b\u5ea6\u8fdb\u884c\u7b5b\u9009<\/span><\/code><code><span class=\"code-snippet_outer\"># \u4f7f\u7528genefilter\u5305\u4e2d\u7684`rowVars`\u51fd\u6570\u8ba1\u7b97\u6bcf\u4e2a\u57fa\u56e0\u7684\u65b9\u5dee\uff08\u53d8\u5f02\u7a0b\u5ea6\uff09\uff0c<\/span><\/code><code><span class=\"code-snippet_outer\"># \u7136\u540e\u9009\u62e9\u65b9\u5dee\u5927\u4e8e\u6307\u5b9a\u9608\u503c\u7684\u57fa\u56e0\u4f5c\u4e3a\u7b5b\u9009\u7ed3\u679c\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">> threshold_var <- 0.1 # \u8bbe\u7f6e\u65b9\u5dee\u7684\u9608\u503c<\/span><\/code><code><span class=\"code-snippet_outer\">> selected_genes_by_var <- gene_expr[rowVars(gene_expr) > threshold_var, ]<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"># \u53ef\u89c6\u5316\uff1a\u7bb1\u7ebf\u56fe\u6bd4\u8f83\u7b5b\u9009\u524d\u540e\u7684\u6570\u636e<\/span><\/code><code><span class=\"code-snippet_outer\">> par(mfrow = c(1, 2))<\/span><\/code><code><span class=\"code-snippet_outer\">> boxplot(gene_expr, col = \"lightblue\", main = \"Before Filtering\", xlab = \"Gene\", ylab = \"Expression\")<\/span><\/code><code><span class=\"code-snippet_outer\">> boxplot(selected_genes_by_var, col = \"lightgreen\", main = \"After Filtering by Variance\", xlab = \"Gene\", ylab = \"Expression\")<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.8598265895953757\" data-s=\"300,640\" data-type=\"png\" data-w=\"692\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-10-02_\u4f7f\u7528R\u8bed\u8a00\u5305genefilter\u9884\u5904\u7406\u6570\u636e\u548c\u7b5b\u9009\u6570\u636e\u7684\u4fdd\u59c6\u7ea7\u6559\u7a0b\/5_I1rkkLYhHzU58kuUbnzYSlsm075UzQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxkQdNGeWtDGfzAUzolwgtQnpAP1XEe22MfUxMxxj5j3OlJI1rkkLYhHzU58kuUbnzYSlsm075UzQ\/640?wx_fmt=png'\" \/><\/p>\n<p><br \/><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528\u4e86\u4e24\u79cd\u7b5b\u9009\u65b9\u6cd5\uff1a\u57fa\u4e8e\u6807\u51c6\u5dee\uff08\u8868\u8fbe\u6a21\u5f0f\uff09\u548c\u57fa\u4e8e\u65b9\u5dee\uff08\u53d8\u5f02\u7a0b\u5ea6\uff09\u3002\u901a\u8fc7\u53ef\u89c6\u5316\u7bb1\u7ebf\u56fe\uff0c\u6211\u4eec\u53ef\u4ee5\u76f4\u89c2\u5730\u6bd4\u8f83\u7b5b\u9009\u524d\u540e\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u5206\u5e03\u3002\u901a\u8fc7\u8c03\u6574\u9608\u503c\uff0c\u6211\u4eec\u53ef\u4ee5\u7075\u6d3b\u5730\u9009\u62e9\u9002\u5408\u7279\u5b9a\u7814\u7a76\u95ee\u9898\u7684\u57fa\u56e0\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">genefilter\u8fd8\u652f\u6301\u5e76\u884c\u8ba1\u7b97\uff0c\u8fd9\u4f7f\u5f97\u5904\u7406\u5927\u89c4\u6a21\u6570\u636e\u53d8\u5f97\u66f4\u52a0\u9ad8\u6548\u3002\u5728\u5904\u7406\u5927\u89c4\u6a21\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u65f6\uff0c\u8ba1\u7b97\u590d\u6742\u5ea6\u53ef\u80fd\u975e\u5e38\u9ad8\uff0c\u4f7f\u7528\u5e76\u884c\u8ba1\u7b97\u53ef\u4ee5\u5145\u5206\u5229\u7528\u8ba1\u7b97\u673a\u8d44\u6e90\uff0c\u52a0\u901f\u6570\u636e\u5904\u7406\u8fc7\u7a0b\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u4ee5\u4e0a\u5c31\u662f\u5bf9R\u8bed\u8a00\u5305genefilter\u7684\u7b80\u5355\u4ecb\u7ecd\u5566\uff0c\u5b83\u63d0\u4f9b\u4e86\u6570\u636e\u9884\u5904\u7406\u548c\u7b5b\u9009\u529f\u80fd\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u4ece\u6d77\u91cf\u7684\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u4e2d\u6316\u6398\u51fa\u6709\u610f\u4e49\u7684\u4fe1\u606f\uff0c\u4e3a\u751f\u7269\u5b66\u7814\u7a76\u63d0\u4f9b\u6709\u529b\u7684\u652f\u6301\u3002\u65e0\u8bba\u662f\u5728\u751f\u7269\u533b\u5b66\u7814\u7a76\u3001\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u8fd8\u662f\u57fa\u56e0\u7ec4\u5b66\u7814\u7a76\u9886\u57df\uff0cgenefilter\u90fd\u662f\u4e00\u4e2a\u975e\u5e38\u6709\u4ef7\u503c\u7684\u5de5\u5177\uff0c\u6709\u52a9\u4e8e\u52a0\u5feb\u7814\u7a76\u8fdb\u5c55\uff0c\u4fc3\u8fdb\u751f\u7269\u5b66\u9886\u57df\u7684\u53d1\u5c55\u3002<o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><br \/><\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;color: rgb(0, 0, 0);\">\u5c0f\u4f19\u4f34\u4eec\uff0c\u4eca\u5929\u6709\u6ca1\u6709\u5b66\u5230\u65b0\u77e5\u8bc6\u5462\uff0c\u60f3\u8981\u7ee7\u7eed\u4e86\u89e3R\u8bed\u8a00\u5185\u5bb9\u53ef\u4ee5\u6301\u7eed\u5173\u6ce8\u5c0f\u679c\u54e6\uff5e<\/span><\/p>\n<p><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;color: rgb(0, 0, 0);\">\u6216\u8005\u4e5f\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u5b98\u7f51\u4e5f\u4f1a\u6301\u7eed\u66f4\u65b0\u7684\u54e6\uff5e <\/span><\/p>\n<section style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;text-align: left;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 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textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/a><br \/><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491909&idx=1&sn=902e34bcf53e605fba2b457ec6a33e36&chksm=cf7f7180f808f8961542f458a49da14e85d8831449fb65fbf2623d55affc564686a5422f56fd&scene=21#wechat_redirect\" textvalue=\"3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\">3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8<\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" 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