{"id":60232,"date":"2024-06-17T11:03:57","date_gmt":"2024-06-17T03:03:57","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60232"},"modified":"2024-06-17T11:03:57","modified_gmt":"2024-06-17T03:03:57","slug":"tidybulk-%e6%91%88%e5%bc%83%e7%b9%81%e7%90%90%e4%bb%a3%e7%a0%81%ef%bc%8c%e5%9c%a8%e5%b7%a8%e4%ba%ba%e8%82%a9%e8%86%80%e5%ad%a6%e4%b9%a0%e8%bd%ac%e5%bd%95%e7%bb%84%ef%bc%88%e4%ba%8c%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60232","title":{"rendered":"tidybulk\u2014\u6448\u5f03\u7e41\u7410\u4ee3\u7801\uff0c\u5728\u5de8\u4eba\u80a9\u8180\u5b66\u4e60\u8f6c\u5f55\u7ec4\uff08\u4e8c\uff09"},"content":{"rendered":"


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\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar 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rich_media_meta_text\">\u5c0f\u679c  <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c  <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-12-14 19:00:11<\/em><\/div>\n<p><content><\/p>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013568\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g-70.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"font-family: \u5b8b\u4f53;font-size: var(--articleFontsize);letter-spacing: 0.578px;text-align: center;\" data-recalc-dims=\"1\"><span style=\"font-size: 15px;font-family: \u5b8b\u4f53;letter-spacing: 0.034em;\">\u4eca\u5929\u5c0f\u679c\u6765\u548c\u4e00\u8d77\u5b66\u4e60tidybulk\u5305\u7684\u7b2c\u4e8c\u8282\u3002\u4e0d\u77e5\u9053\u5927\u5bb6\u6709\u6ca1\u6709\u770b\u5b8c\u5c0f\u679c\u7b2c\u4e00\u8282\u7684\u8bb2\u89e3\u5462\uff1f\u5982\u679c\u8fd8\u6ca1\u6709\u7684\u8bdd\uff0c\u53ef\u4ee5\u8fdb\u5165\u516c\u4f17\u53f7\u4e00\u5b66\u4e60\u4e00\u4e0b\u524d\u9762\u7684\u5185\u5bb9\u54e6~ \u5c0f\u679c\u5728\u7b2c\u4e00\u8282\u4e2d\u4e3a\u5927\u5bb6\u8bb2\u89e3\u4e86\u8f6c\u5f55\u7ec4\u5206\u6790\u7684\u884c\u540d\u6574\u5408\uff0c\u6570\u636e\u7684\u6807\u51c6\u5316\uff0c\u7b5b\u9009\u5dee\u5f02\u57fa\u56e0\u4ee5\u53ca\u964d\u7ef4\u90e8\u5206\u7684\u4ee3\u7801\u3002\u8fd9\u4e9b\u5728\u8f6c\u5f55\u7ec4\u5b66\u7684\u5206\u6790\u4e2d\u90fd\u662f\u5341\u5206\u91cd\u8981\u7684\u5185\u5bb9\u54e6~\u56e0\u6b64\u5c0f\u679c\u5728\u7b2c\u4e8c\u7ae0\u4e2d\u4e5f\u4f1a\u7701\u7565\u4e00\u90e8\u5206\u91cd\u590d\u7684\u5185\u5bb9\u54e6\uff0c\u5f53\u7136\u5c0f\u679c\u4e5f\u4f1a\u8fdb\u884c\u76f8\u5e94\u7684\u6ce8\u91ca\uff0c\u5b9e\u5728\u6709\u4e0d\u61c2\u7684\u5c0f\u4f19\u4f34\u7ffb\u770b\u4e00\u4e0b\u7b2c\u4e00\u8282\u5462\u3002\u597d\u5566~\u90a3\u73b0\u5728\u5c31\u8ba9\u5c0f\u679c\u966a\u7740\u5927\u5bb6\u4e00\u8d77\u5f00\u59cb\u4eca\u5929\u7b2c\u4e8c\u8282\u7684\u5b66\u4e60\u5427\uff01<br \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u52a0\u8f7dR\u5305<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5982\u679c\u662f\u4e24\u8282\u4e00\u8d77\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u8fd9\u4e00\u6b65\u5c31\u53ef\u4ee5\u7701\u7565\u5566~<\/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<\/ul>\n<pre class=\"code-snippet__js\"><code><span class=\"code-snippet_outer\">library(tidyverse)<\/span><\/code><code><span class=\"code-snippet_outer\">library(tidybulk)<\/span><\/code><code><span class=\"code-snippet_outer\">library(SummarizedExperiment)<\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u5dee\u5f02\u5206\u6790<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u6b63\u5982\u5c0f\u679c\u4e0a\u8282\u6240\u8bb2\u7684\uff0c\u6211\u4eec\u505a\u8f6c\u5f55\u7ec4\u5206\u6790\u60f3\u8981\u7814\u7a76\u7684\u6700\u4e3b\u8981\u7684\u4e00\u4e2a\u65b9\u5411\u5c31\u662f\u4e0d\u540c\u6837\u672c\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c\u8fd9\u4e00\u8282\u5c31\u662f\u5728\u7814\u7a76\u8fd9\u4e00\u4e2a\u65b9\u5411\u3002\u5728\u6211\u4eec\u73b0\u6709\u7684\u7814\u7a76\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528edgeR\u6216\u662flimma\u7b49\u8f6f\u4ef6\u8fdb\u884c\u8ba1\u7b97\u3002\u901a\u8fc7test_differential_abundance\u51fd\u6570\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u5f97\u51fa\u4e00\u4e2a\u5305\u542b\u5bf9\u6570\u500d\u6570\u53d8\u5316\uff0cp-value\u7684tibble\u6587\u4ef6\u3002\u63a5\u4e0b\u968f\u7740\u5c0f\u679c\u7684\u6b65\u4f10\u4e00\u8d77\u6765\u770b\u770b\u5982\u4f55\u4f7f\u7528tidybulk\u5305\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u5427\uff01<\/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<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u8fd9\u91cc\u76f8\u5f53\u4e8e\u5176\u4e2d\u7684\u4e00\u4e2a\u6837\u672c\u548c\u5176\u4f59\u7684\u6240\u6709\u6837\u672c\u8fdb\u884c\u5bf9\u6bd4 <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.de = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> test_differential_abundance( ~ condition, action=\"get\") <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.de %>% tidySummarizedExperiment::as_tibble() -> res1 <\/span><\/code><code><span class=\"code-snippet_outer\">head(res1)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 13 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .feature .sample count Cell.type time condition batch factor_of_interest <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 A1BG SRR1740034 153 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 A1BG-AS1 SRR1740034 83 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 AAAS SRR1740034 868 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 AACS SRR1740034 222 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 AAGAB SRR1740034 590 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 AAMDC SRR1740034 48 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u6dfb\u52a0.contrasts\u53c2\u6570\u8fc7\u540e\uff0c\u5c0f\u679c\u5728\u8fd9\u6307\u5b9a\u4e86\u4e24\u4e2a\u6837\u672c\u8fdb\u884c\u5dee\u5f02\u5206\u6790\u3002<\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.de.contr = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> identify_abundant(factor_of_interest = condition) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> test_differential_abundance(~0+ condition, .contrasts =c( \"conditionFALSE - conditionTRUE\"), <\/span><\/code><code><span class=\"code-snippet_outer\"> action=\"get\" <\/span><\/code><code><span class=\"code-snippet_outer\"> )<\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.de.contr %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> tidySummarizedExperiment::as_tibble() -> res2 <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">head(res2)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 14 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .feature .sample count Cell.type time condition batch factor_of_interest <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 A1BG SRR1740034 153 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 A1BG-AS1 SRR1740034 83 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 AAAS SRR1740034 868 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 AACS SRR1740034 222 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 AAGAB SRR1740034 590 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 AAMDC SRR1740034 48 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u53bb\u6279\u6b21<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5f53\u8fdb\u884c\u8f6c\u5f55\u7ec4\u7684\u6570\u636e\u6574\u5408\u7684\u65f6\u5019\uff0c\u6d4b\u5e8f\u7684\u6279\u6b21\u4f1a\u5bf9\u6570\u636e\u53ef\u80fd\u4f1a\u6709\u4e00\u5b9a\u7684\u5f71\u54cd\uff0c\u8fd9\u65f6\u5019\u5404\u4f4d\u5c0f\u4f19\u4f34\u5c31\u9700\u8981\u8fdb\u884c\u53bb\u6279\u6b21\u7684\u5904\u7406\uff01<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u6570\u636e\u7684\u51c6\u5907\uff0c\u8fd9\u91cc\u5728\u7b2c\u4e00\u8282\u4e2d\u5df2\u7ecf\u8fd0\u884c\u8fc7\u5566\uff0c\u4e0d\u8fc7\u4e3a\u4e86\u5206\u5f00\u4e24\u8282\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\uff0c\u5c0f\u679c\u5728\u8fd9\u5c31\u91cd\u590d\u4e00\u4e0b\u4ee3\u7801\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u76f4\u63a5\u8dd1\u5c31\u53ef\u4ee5\u5566 <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">rowData(counts_SE)$<\/span>gene_name =rownames(counts_SE) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.aggr = counts_SE %>%aggregate_duplicates(.transcript = gene_name)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># tidybulk says: your object does not have duplicates along the gene_name column. The input dataset is returned.<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm = counts_SE.aggr %>%identify_abundant(factor_of_interest = condition) %>%scale_abundance()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># tidybulk says: the sample with largest library size SRR1740080 was chosen as reference for scaling<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u5728\u8fd9\u4e00\u6b65\u4e2d\u53ef\u80fd\u9700\u8981\u4e0b\u8f7dR\u5305\uff0c\u90a3\u56e0\u4e3a\u73af\u5883\u4e0d\u4e00\u6837\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ea\u9700\u8981\u6839\u636e\u63d0\u793a\u8fdb\u884cR\u5305\u7684\u5b89\u88c5\u5c31\u53ef\u4ee5\u5566\uff0c\u5982\u679c\u9047\u5230\u4e0d\u597d\u89e3\u51b3\u7684\u95ee\u9898\uff0c\u4e5f\u53ef\u4ee5\u5728\u8bc4\u8bba\u7559\u8a00\uff0c\u5c0f\u679c\u770b\u5230\u540e\u4e5f\u4f1a\u4e3a\u5927\u5bb6\u7684\u95ee\u9898\u8fdb\u884c\u4e00\u4e00\u89e3\u7b54\u54e6! <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.adj = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm %>%adjust_abundance( ~ factor_of_interest + batch)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Found2batches<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Adjusting for1covariate(s) or covariate level(s)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Standardizing Data across genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Fitting L\/S model and finding priors<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Finding parametric adjustments<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Adjusting the Data<\/span><\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u5377\u79ef\u5206\u8fa8\u7ec6\u80de\u7c7b\u578b\uff08\u673a\u5668\u5b66\u4e60\uff09<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u5728\u8f6c\u5f55\u7ec4\u5b66\u7684\u7814\u7a76\u4e2d\uff0c\u7ec6\u80de\u7c7b\u578b\u7684\u786e\u5b9a\u662f\u5f88\u5173\u952e\u7684\u4e00\u9879\uff0c\u5728\u8fd9\u4e2aR\u5305\u4e2d\uff0c\u4e3a\u5404\u4f4d\u5c0f\u4f19\u4f34\u63d0\u4f9b\u4e86\u4e00\u4e2a\u5927\u5bb6\u53ef\u80fd\u5e73\u65f6\u4e0d\u592a\u4f1a\u63a5\u89e6\u5230\u7684\u786e\u5b9a\u7ec6\u80de\u7c7b\u578b\u7684\u65b9\u6cd5\uff0c\u90a3\u5c31\u662f\u5377\u79ef\uff0c\u4f46\u5982\u679c\u8981\u8bb2\u89e3\u5377\u79ef\u5177\u4f53\u662f\u4ec0\u4e48\u4e1c\u897f\u5c31\u4f1a\u6d89\u53ca\u5230\u5f88\u591a\u5185\u5bb9\u5566\uff0c\u5c0f\u679c\u4eca\u5929\u5c31\u4e0d\u8be6\u7ec6\u4ecb\u7ecd\u5566\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u901a\u8fc7\u67e5\u770b\u516c\u4f17\u53f7\u7684\u5176\u4ed6\u63a8\u6587\u8fdb\u884c\u5b66\u4e60\u54e6~ \u90a3\u4e48\u4e0b\u9762\u5c31\u8ba9\u5c0f\u679c\u53ef\u4ee5\u5b9e\u64cd\u5427\uff01<\/span>    <\/span><span style=\"background-color: rgb(248, 248, 248);font-family: Consolas;font-size: 15px;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"typescript\"><code><span class=\"code-snippet_outer\">counts_SE.cibersort = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> deconvolve_cellularity(action=<span class=\"code-snippet__string\">\"get\"<\/span>, cores=<span class=\"code-snippet__number\">1<\/span>, prefix =<span class=\"code-snippet__string\">\"cibersort__\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.cibersort %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_longer( <\/span><\/code><code><span class=\"code-snippet_outer\"> names_to=<span class=\"code-snippet__string\">\"Cell_type_inferred\"<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> values_to =<span class=\"code-snippet__string\">\"proportion\"<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> names_prefix =<span class=\"code-snippet__string\">\"cibersort__\"<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> cols=contains(<span class=\"code-snippet__string\">\"cibersort__\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\"> ) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(x=<span class=\"code-snippet__string\">`Cell_type_inferred`<\/span>, y=proportion, fill=<span class=\"code-snippet__string\">`Cell.type`<\/span>)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_boxplot() + <\/span><\/code><code><span class=\"code-snippet_outer\"> facet_wrap(~<span class=\"code-snippet__string\">`Cell.type`<\/span>) + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme(axis.text.x =element_text(angle =<span class=\"code-snippet__number\">90<\/span>, hjust =<span class=\"code-snippet__number\">1<\/span>, vjust =<span class=\"code-snippet__number\">0.5<\/span>), aspect.ratio=<span class=\"code-snippet__number\">1<\/span>\/<span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">## tidySummarizedExperiment says: A data frame is returned <span class=\"code-snippet__keyword\">for<\/span> independent data analysis. <\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013569\" data-ratio=\"0.8\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_pIjMOZciasJF7zz4wnmxAplTSjotPw.png?resize=480%2C384\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXAgxy1eztEXiaHW5Q2lxorvE96icpIjMOZciasJF7zz4wnmxAplTSjotPw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384 .7799987792969\" width=\"480 .969970703125\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"># \u5dee\u5f02\u7ec6\u80de\u7c7b\u578b\u7684\u4e30\u5ea6\u8ba1\u7b97 tidybulk\u5305\u53ef\u4ee5\u5bf9\u4e0d\u540c\u6761\u4ef6\u4e0b\u7684\u5dee\u5f02\u7ec6\u80de\u7c7b\u578b\u4e30\u5ea6\u8fdb\u884c\u7edf\u8ba1\u6d4b\u8bd5\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> test_differential_cellularity(. ~ condition ) %>%head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 7 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .cell_type cell_type_proportions `estimate_(Intercept)` estimate_conditionTRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 cibersort\u2026 -2.94 2.25 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 cibersort\u2026 -4.86 1.48 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 cibersort\u2026 -5.33 -0.487 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 cibersort\u2026 -2.33 0.924 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 cibersort\u2026 -2.83 -0.620 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 cibersort\u2026 -2.46 0.190 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 3 more variables: std.error_conditionTRUE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # statistic_conditionTRUE, p.value_conditionTRUE<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u7d27\u8ddf\u7740\uff0c\u8fd8\u53ef\u4ee5\u4f7f\u7528\u5f97\u5230\u7684\u6570\u636e\u8fdb\u884c\u56de\u5f52\u5206\u6790\u3002<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE_survival = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> nest(data =-sample) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> mutate( <\/span><\/code><code><span class=\"code-snippet_outer\"> days =sample(1:1000, size =n()), <\/span><\/code><code><span class=\"code-snippet_outer\"> dead =sample(c(0,1), size =n(), replace =TRUE) <\/span><\/code><code><span class=\"code-snippet_outer\"> ) %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> unnest(data) <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE_survival %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> test_differential_cellularity(survival::Surv(days, dead) ~ .) %>%head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 6 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .cell_type cell_type_proportions estimate std.error statistic p.value <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 cibersort.B.cells.\u2026 0.379 0.685 0.554 0.580 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 cibersort.B.cells.\u2026 0.201 0.346 0.581 0.561 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 cibersort.Plasma.c\u2026 -3.34 1.02 -3.28 0.00102 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 cibersort.T.cells.\u2026 -2.58 1.69 -1.53 0.127 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 cibersort.T.cells.\u2026 0.0698 0.513 0.136 0.892 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 cibersort.T.cells.\u2026 0.383 0.493 0.778 0.437<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013595\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-13.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: 15px;letter-spacing: 0.578px;text-wrap: wrap;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: center;\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u63a5\u7740\u5c0f\u679c\u4f1a\u5e26\u7740\u5927\u5bb6\u8fdb\u884cKaplan-Meier \u66f2\u7ebf\u7684\u68c0\u9a8c\u5e76\u8fdb\u884c\u53ef\u89c6\u5316\u3002<\/span><span style=\"background-color: rgb(248, 248, 248);font-family: Consolas;font-size: 15px;text-align: left;text-indent: 0pt;letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_stratified = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE_survival %>% <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> # Test <\/span><\/code><code><span class=\"code-snippet_outer\"> test_stratification_cellularity( <\/span><\/code><code><span class=\"code-snippet_outer\"> survival::Surv(days, dead) ~ ., <\/span><\/code><code><span class=\"code-snippet_outer\"> sample, transcript, count <\/span><\/code><code><span class=\"code-snippet_outer\"> ) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">head(counts_stratified)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 6 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .cell_type cell_type_proportions .low_cellularity_exp\u2026\u00b9 .high_cellularity_ex\u2026\u00b2 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 cibersort\u2026 11.3 11.7 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 cibersort\u2026 17.7 5.32 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 cibersort\u2026 13.3 9.72 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 cibersort\u2026 13.8 9.25 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 cibersort\u2026 10.7 12.3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 cibersort\u2026 13.6 9.45 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 abbreviated names: \u00b9.low_cellularity_expected, \u00b2.high_cellularity_expected <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 2 more variables: pvalue, plot<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">counts_stratified$<\/span>plot[[1]] <\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013565\" data-ratio=\"0.8\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_j5lxliaEzXVv2Faq2FGb2sdmic7baQ.png?resize=480%2C384\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXdNwiaQapBS6IK3KnDyUP4TwqnDNj5lxliaEzXVv2Faq2FGb2sdmic7baQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384 .7799987792969\" width=\"480 .969970703125\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u805a\u7c7b<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u5404\u4f4d\u5c0f\u4f19\u4f34\u7684\u8f6c\u5f55\u7ec4\u5b66\u7814\u7a76\u4e2d\uff0c\u76f8\u4fe1\u5927\u5bb6\u4e00\u5b9a\u5bf9\u805a\u7c7b\u95ee\u9898\u4e0d\u964c\u751f\uff0c\u6210\u529f\u7684\u805a\u7c7b\uff0c\u53ef\u4ee5\u8ba9\u7814\u7a76\u4eba\u5458\u770b\u51fa\u4e2a\u7ec6\u80de\u95f4\u7684\u5f02\u540c\u70b9\uff0ctidybulk\u5305\u4e2d\u4e3a\u5404\u4f4d\u51c6\u5907\u4e86\u4e24\u79cd\u805a\u7c7b\u7684\u65b9\u6cd5\uff0c\u5206\u522b\u662fK-means\u548cSNN\uff08\u4f46SNN\u76ee\u524dR\u5305\u56e0Matrix\u7684\u66f4\u65b0\u53d1\u751f\u62a5\u9519\uff0c\u6682\u4e0d\u53ef\u4f7f\u7528\uff09\uff0c\u4e0b\u9762\u5c31\u8ba9\u5c0f\u679c\u6765\u4e3a\u5927\u5bb6\u5206\u522b\u5b9e\u64cd\u4e00\u4e0b\u3002<\/span><\/p>\n<h2><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>K-means   <\/strong><\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fd9\u91cc\u5c0f\u679c\u4f1a\u7528\u5230\u4e0a\u4e00\u8282\u4e2d\u7684\u964d\u7ef4\u7ed3\u679c <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.MDS = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> reduce_dimensions(method=<span class=\"code-snippet__string\">\"MDS\"<\/span>, .dims =<span class=\"code-snippet__number\">6<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## Getting the 500 most variable genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## tidybulk says: to access the raw results do `attr(..., \"internals\")$MDS`<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.cluster = counts_SE.norm.MDS %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> cluster_elements(method=<span class=\"code-snippet__string\">\"kmeans\"<\/span>, centers =<span class=\"code-snippet__number\">2<\/span>, action=<span class=\"code-snippet__string\">\"get\"<\/span> ) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u53ef\u4ee5\u5c06\u805a\u7c7b\u6ce8\u91ca\u6dfb\u52a0\u5230 MDS \u964d\u7ef4\u6570\u636e\u96c6\u548c\u7ed8\u56fe\u4e2d\u3002 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm.cluster %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(<span class=\"code-snippet__keyword\">x<\/span>=<span class=\"code-snippet__string\">`Dim1`<\/span>, <span class=\"code-snippet__keyword\">y<\/span>=<span class=\"code-snippet__string\">`Dim2`<\/span>, color=<span class=\"code-snippet__string\">`cluster_kmeans`<\/span>)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_point() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw() <\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013566\" data-ratio=\"0.8\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_4xoLDsc8AdyBgfTJululaugATDtARw.png?resize=480%2C384\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXOR3VD2wt2WkcR8AgF8MdPrxm4xoLDsc8AdyBgfTJululaugATDtARw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384 .77996826171875\" width=\"480 .969970703125\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u53bb\u9664\u5197\u4f59\u6570\u636e<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-size: 15px;font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u5728\u7814\u7a76\u7684\u8fc7\u7a0b\u4e2d\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ef\u80fd\u4f1a\u5e0c\u671b\u4ece\u539f\u59cb\u6570\u636e\u96c6\u4e2d\u5220\u9664\u5197\u4f59\u7684\u4e00\u4e9b\u6570\u636e\uff0c\u4f5c\u8005\u4e5f\u60f3\u5230\u4e86\u8fd9\u70b9\uff0c\u4e3a\u5927\u5bb6\u51c6\u5907\u4e86\u5bf9\u5e94\u7684\u51fd\u6570\u3002\u6709\u4e24\u79cd\u65b9\u6cd5\uff1a\u65b9\u6cd5\u4e00\uff1a\u901a\u8fc7\u4f7f\u7528method=\u201ccorrelation\u201d\u53c2\u6570\u5220\u9664\u9ad8\u5ea6\u76f8\u5173\u7684\u7c07\uff08\u4fdd\u7559\u5177\u6709\u4ee3\u8868\u6027\u7684\u7c07\uff09 \u65b9\u6cd5\u4e8c\uff1a\u5728\u964d\u7ef4\u7a7a\u95f4\u4e2d\u79fb\u9664\u6700\u8fd1\u7684\u5143\u7d20\u5bf9\u3002## \u65b9\u6cd51<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\">counts_SE.norm.non_redundant = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm.MDS %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> remove_redundancy( method =<span class=\"code-snippet__string\">\"correlation\"<\/span> )<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## Getting the 8513 most variable genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.non_redundant %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(<span class=\"code-snippet__keyword\">x<\/span>=<span class=\"code-snippet__string\">`Dim1`<\/span>, <span class=\"code-snippet__keyword\">y<\/span>=<span class=\"code-snippet__string\">`Dim2`<\/span>, color=<span class=\"code-snippet__string\">`Cell.type`<\/span>)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_point() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw() <\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013567\" data-ratio=\"0.8\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_rylQKsDcdsKOsxZtS1nqMicspHYDag.png?resize=480%2C384\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXHtKc64010d50IwFjO0fh33HGLrylQKsDcdsKOsxZtS1nqMicspHYDag\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384 .77996826171875\" width=\"480 .969970703125\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<h2><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u65b9\u6cd52 <\/strong><\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"javascript\"><code><span class=\"code-snippet_outer\">counts_SE.norm.non_redundant = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm.MDS %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> remove_redundancy( <\/span><\/code><code><span class=\"code-snippet_outer\"> method =<span class=\"code-snippet__string\">\"reduced_dimensions\"<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> Dim_a_column =<span class=\"code-snippet__string\">`Dim1`<\/span>, <\/span><\/code><code><span class=\"code-snippet_outer\"> Dim_b_column =<span class=\"code-snippet__string\">`Dim2`<\/span> <\/span><\/code><code><span class=\"code-snippet_outer\"> ) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.non_redundant %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(x=<span class=\"code-snippet__string\">`Dim1`<\/span>, y=<span class=\"code-snippet__string\">`Dim2`<\/span>, color=<span class=\"code-snippet__string\">`Cell.type`<\/span>)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_point() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw() <\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013570\" data-ratio=\"0.8\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_sQXQBvVFmqIqvLsjCUBCzWAovlBvQw.png?resize=480%2C384\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXNe8nstzmRR6Q3pictckBfuAg3sQXQBvVFmqIqvLsjCUBCzWAovlBvQw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384 .7799987792969\" width=\"480 .969970703125\" data-recalc-dims=\"1\" \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u5176\u4ed6\u5305\u88c5\u51fd\u6570<br \/>\n  <\/strong><\/span><\/h1>\n<h2><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u4eceBAM\/SAM\u5230\u57fa\u56e0\u8ba1\u6570\u7684\u8f6c\u6362<\/span>   <\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">counts<\/span> =<span class=\"code-snippet__string\">tidybulk_SAM_BAM( <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__meta\">file_names,<\/span> <span class=\"code-snippet__string\"><\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__attr\">genome<\/span> =<span class=\"code-snippet__string\">\"hg38\", <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__attr\">isPairedEnd<\/span> =<span class=\"code-snippet__string\">TRUE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__attr\">requireBothEndsMapped<\/span> =<span class=\"code-snippet__string\">TRUE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__attr\">checkFragLength<\/span> =<span class=\"code-snippet__string\">FALSE, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__attr\">useMetaFeatures<\/span> =<span class=\"code-snippet__string\">TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attr\">)<\/span><\/span><\/code><\/pre>\n<\/section>\n<h2><span style=\"color: rgb(64, 118, 0);font-size: 15px;font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>ensembleID\u548csymbolID\u4e4b\u95f4\u7684\u8f6c\u6362   <\/strong><\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_ensembl %>%ensembl_to_symbol(ens) %>%head()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 8 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># ens iso `read count` sample cases_0_project_dise\u2026\u00b9 cases_0_samples_0_sa\u2026\u00b2 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 ENSG0\u2026 13 144 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 ENSG0\u2026 13 72 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 ENSG0\u2026 13 0 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 ENSG0\u2026 13 1099 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 ENSG0\u2026 13 11 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 ENSG0\u2026 13 2 TARGE\u2026 Acute Myeloid Leukemia Primary Blood Derived\u2026 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 abbreviated names: \u00b9cases_0_project_disease_type, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u00b2cases_0_samples_0_sample_type <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 2 more variables: transcript, ref_genome <\/span><\/span><\/code><\/pre>\n<\/section>\n<h2><span style=\"color: rgb(64, 118, 0);\"><strong><span style=\"font-size: 15px;\"><span style=\"font-family: Calibri;font-variant: normal;text-transform: none;\">symbol\u548c\u57fa\u56e0\u5168\u540d\u4e4b\u95f4\u7684\u8f6c\u6362<\/span>  <\/span><\/strong><\/span><span style=\"font-size: 15px;\"> <\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> describe_transcript() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> select(feature, description, everything()) %>%print(n =5)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A SummarizedExperiment-tibble abstraction: 408,624 \u00d7 48 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # [90mFeatures=8513 | Samples=48 | Assays=count[0m <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># feature sample count Cell.type time condition batch factor_of_interest <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 A1BG SRR1740034 153 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 A1BG-AS1 SRR1740034 83 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 AAAS SRR1740034 868 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 AACS SRR1740034 222 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 AAGAB SRR1740034 590 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 AAMDC SRR1740034 48 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 7 AAMP SRR1740034 1257 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 8 AANAT SRR1740034 284 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 9 AAR2 SRR1740034 379 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 10 AARS2 SRR1740034 685 b_cell 0 d TRUE 0 TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 40 more rows <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 2 more variables: description, gene_name<\/span><\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5230\u6b64tidybulk\u5305\u5c31\u5df2\u7ecf\u5168\u90e8\u8bb2\u89e3\u5b8c\u6bd5\u5566~\u7ed9\u5c0f\u679c\u7684\u611f\u89c9\uff0c\u8fd9\u6b3eR\u5305\u771f\u7684\u662f\u4e00\u4e2a\u5f88\u5168\u9762\uff0c\u800c\u4e14\u5bf9\u4e8e\u65b0\u624b\u975e\u5e38\u6709\u5e2e\u52a9\u7684R\u5305\uff0c\u8877\u5fc3\u5e0c\u671b\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ef\u4ee5\u8ba4\u771f\u7684\u5b66\u4e60\u4e00\u4e0b\u54e6\uff01<\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<p><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497335&idx=2&sn=b9bd1327156243517c611c7c071a2de6&chksm=cf7f66b2f808efa472e6930865ed8da7fbaa600ed58351f035314ce545b26ea32fb9311a8faf&scene=21#wechat_redirect\" textvalue=\"\u4f60\u5df2\u9009\u4e2d\u4e86\u6dfb\u52a0\u94fe\u63a5\u7684\u5185\u5bb9\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span style=\"font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-size: 15px;\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013695\" data-ratio=\"0.35444444444444445\" 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0.034em;caret-color: rgba(0, 0, 0, 0);\" data-recalc-dims=\"1\"><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;text-wrap: wrap;outline: 0px;font-family: system-ui, -apple-system, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;background-color: rgb(255, 255, 255);text-align: left;\">\n<section style=\"outline: 0px;font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;outline: 0px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;outline: 0px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;outline: 0px;\">\n<section style=\"outline: 0px;display: inline-block;width: 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