{"id":30174,"date":"2024-02-28T18:05:39","date_gmt":"2024-02-28T10:05:39","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30174"},"modified":"2024-02-28T18:05:40","modified_gmt":"2024-02-28T10:05:40","slug":"%e7%83%ad%e5%9b%be-%e7%94%9f%e6%88%90%e4%bd%a0%e7%9a%84%e5%8d%95%e7%bb%86%e8%83%9e%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be%e8%b0%83%e8%89%b2%e6%9d%bf","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30174","title":{"rendered":"\u70ed\u56fe-\u751f\u6210\u4f60\u7684\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u201c\u8c03\u8272\u677f\u201d"},"content":{"rendered":"<p><strong>\u70ed\u56fe-\u751f\u6210\u4f60\u7684\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u201c\u8c03\u8272\u677f\u201d<\/strong><\/p>\n<p>\u5f53\u6211\u4eec\u751f\u6210\u5355\u7ec6\u80de\u7684\u6570\u636e\u77e9\u9635\u5e76\u4e86\u89e3\u4e86\u7ec6\u80de\u4e2d\u57fa\u56e0\u8868\u8fbe\u7684\u57fa\u672c\u60c5\u51b5\u540e\uff0c\u6211\u4eec\u8981\u5982\u4f55\u6574\u4f53\u89c2\u5bdf\u7ec6\u80de\u95f4\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u76f8\u5173\u6027\u5462\uff1f\u5927\u5bb6\u4e00\u8d77\u6765\u548c\u5c0f\u679c\u770b\u4e00\u4e0b\u5427\uff01<\/p>\n<ul>\n<li><strong>\u6570\u636e\u51c6\u5907<\/strong><\/li>\n<\/ul>\n<p>library(scRNAseq)<br \/>\ndata(fluidigm)<br \/>\nfluidigm&lt;-ReprocessedFluidigmData()<br \/>\nct &lt;- floor(assays(fluidigm)$rsem_counts) #\u751f\u6210\u6570\u636e\u77e9\u9635<br \/>\nct[1:4,1:4]<br \/>\nsample_ann &lt;- as.data.frame(colData(fluidigm))<br \/>\nDT::datatable(sample_ann)<br \/>\nView(ct)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"298\" class=\"wp-image-30175\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=640%2C298\" alt=\"\u8868\u683c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?w=1927 1927w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=300%2C140 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=1024%2C477 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=768%2C357 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=1536%2C715 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?resize=600%2C279 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-113.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u9996\u5148\uff0c\u6211\u4eec\u5148\u6765\u4e00\u8d77\u770b\u4e00\u4e0b\u751f\u6210\u7684\u6570\u636e\u77e9\u9635\uff1a<\/p>\n<ul>\n<li><strong>\u6570\u636e\u8fc7\u6ee4<\/strong><\/li>\n<\/ul>\n<p>\u5728\u67e5\u770b\u57fa\u56e0\u5728\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u76f8\u5173\u6027\u4e4b\u524d\uff0c\u6211\u4eec\u5148\u5bf9\u6570\u636e\u505a\u4e00\u4e2a\u7b80\u5355\u7684\u7b5b\u9009\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u7b5b\u9009\u51fa\u6240\u6709\u8868\u8fbe\u7ec6\u80de\u6570\u5927\u4e8e0\u7684\u57fa\u56e0\uff0c\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5177\u4f53\u64cd\u4f5c\u5427\uff01<\/p>\n<p>chose_gene= apply(counts,1,function(x) sum(x&gt;0) )&gt;0<br \/>\ntable(chose_gene)<br \/>\ncounts &lt;- counts[chose_gene,]<br \/>\ntable((apply(counts,1,function(x) sum(x&gt;0)&gt;0 )))<\/p>\n<ul>\n<li><strong>\u7ed8\u5236\u70ed\u56fe<\/strong><\/li>\n<\/ul>\n<p>\u6ca1\u9519\uff0c\u73b0\u5728\u6211\u4eec\u6765\u5230\u4e86\u4eca\u5929\u7684\u91cd\u5934\u620f\uff0c\u90a3\u5c31\u662f\u901a\u8fc7\u70ed\u56fe\u6765\u89c2\u5bdf\u57fa\u56e0\u5728\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u76f8\u5173\u6027\u548c\u5dee\u5f02\u6027\uff0c\u90a3\u4e48\u4ec0\u4e48\u662f\u70ed\u56fe\u5462\uff1f\u5728\u7ed8\u5236\u4e4b\u524d\u5c0f\u679c\u5148\u7ed9\u5927\u5bb6\u505a\u4e00\u4e2a\u7b80\u5355\u7684\u4ecb\u7ecd\uff1a<\/p>\n<ul>\n<li>\n<ul>\n<li><strong>\u70ed\u56fe\u7684\u6982\u5ff5\uff1a<\/strong><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>\u70ed\u56fe(Heatmap)\u662f\u901a\u8fc7\u5c06\u6570\u636e\u77e9\u9635\u4e2d\u7684\u5404\u4e2a\u8868\u8fbe\u503c\u6309\u7167\u4e00\u5b9a\u7684\u89c4\u5f8b\u6620\u5c04\u4e3a\u4e0d\u540c\u7684\u989c\u8272\uff0c\u6700\u7ec8\u5448\u73b0\u7ed9\u6211\u4eec\u4e00\u4e2a\u50cf\u201c\u8c03\u8272\u76d8\u201d\u4e00\u6837\u7684\u56fe\u8868\u6765\u5c55\u793a\u6570\u636e\u7684\u53d8\u5316\u89c4\u5f8b\uff0c\u53ef\u4ee5\u76f4\u63a5\u7f8e\u89c2\u5730\u5411\u6211\u4eec\u8868\u8fbe\u57fa\u56e0\u7684\u5168\u5c40\u8868\u8fbe\u72b6\u51b5\u54e6\u3002<\/p>\n<ul>\n<li>\n<ul>\n<li><strong>\u7ed8\u5236\u70ed\u56fe<\/strong><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>\u8981\u7ed8\u5236\u672c\u6b21\u5b9e\u9a8c\u4e2d\u5bf9\u5e94\u6570\u636e\u77e9\u9635\u7684\u70ed\u56fe\uff0c\u53ea\u9700\u8981\u901a\u8fc7R\u8bed\u8a00\u4e2d\u7684 pheatmap()\u51fd\u6570\u7ed8\u5236\u65b9\u6cd5\u5373\u53ef\uff0c\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u4e00\u4e0b\u5177\u4f53\u7684\u4ee3\u7801\u64cd\u4f5c\u5427\uff01<\/p>\n<p>#\u7ec6\u80de\u4e4b\u95f4\u6240\u6709\u57fa\u56e0\u8868\u8fbe\u91cf\u7684\u76f8\u5173\u6027<br \/>\ndata &lt;- log2(edgeR::cpm(counts) +1)<br \/>\ndata[1:4,1:4]<br \/>\ndata_back &lt;- data<br \/>\nexperSet &lt;- data_back<br \/>\ncolnames(experSet)<br \/>\n#pheatmap \u7ed8\u5236\u70ed\u56fe\u7684\u51fd\u6570<br \/>\npheatmap::pheatmap(cor(experSet))<\/p>\n<p>\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u6700\u7ec8\u5448\u73b0\u51fa\u7684\u70ed\u56fe\u662f\u4ec0\u4e48\u6837\u5427\uff01<\/p>\n<ul>\n<li>\n<ul>\n<li><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"243\" class=\"wp-image-30176\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=640%2C243\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?w=2500 2500w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=300%2C114 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=1024%2C389 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=768%2C292 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=1536%2C583 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=2048%2C777 2048w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?resize=600%2C228 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-2.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><strong>\u600e\u4e48\u5206\u6790\u70ed\u56fe\uff1f<\/strong><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"245\" class=\"wp-image-30177\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?resize=640%2C245\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?w=1449 1449w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?resize=300%2C115 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?resize=1024%2C392 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?resize=768%2C294 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?resize=600%2C229 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-30174-3.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/> \u5f53\u6211\u4eec\u6210\u529f\u7ed8\u5236\u51fa\u7ec6\u80de\u8868\u8fbe\u7684\u70ed\u56fe\u540e\uff0c\u5982\u4f55\u5feb\u901f\u5730\u4ece\u4e2d\u83b7\u53d6\u6709\u6548\u7684\u4fe1\u606f\u5462\uff1f\u4e0d\u8981\u6025\uff0c\u5c0f\u679c\u544a\u8bc9\u4f60\uff01<\/p>\n<p>1.\u6837\u672c\u540d\u79f0\u533a\uff1a\u5206\u4e3a\u53f3\u4fa7\u548c\u4e0b\u65b9\u4e24\u90e8\u5206\uff0c\u5206\u522b\u7ec6\u80de\u540d\u79f0\u548c\u57fa\u56e0\u540d\u79f0\uff1b<\/p>\n<p>2.\u8272\u5757\u5c55\u793a\u533a\uff1a\u6839\u636e\u6837\u672c\u540d\u79f0\u751f\u6210\u7684\u989c\u8272\u77e9\u9635\uff0c\u6bcf\u4e00\u4e2a\u5c0f\u77e9\u5f62\u7684\u8272\u5757 \u90fd\u4ee3\u8868\u4e00\u4e2a\u8868\u8fbe\u6570\u503c\uff1b<\/p>\n<p>3.\u8272\u677f\u5bf9\u7167\u533a\uff1a\u8272\u677f\u4e2d\u7684\u6bcf\u4e00\u4e2a\u989c\u8272\u90fd\u5bf9\u5e94\u5230\u6bcf\u4e00\u4e2a\u77e9\u5f62\u4e2d\u7684\u989c\u8272\u6570\u503c\uff0c\u5728\u672c\u56fe\u7684\u8272\u677f\u5bf9\u7167\u533a\u4e2d\uff0c\u503c\u8d8a\u5927\u8d8a\u7ea2\uff0c\u8d8a\u5c0f\u8d8a\u84dd\u3002<\/p>\n<p>\u73b0\u5728\u4f60\u5b66\u4f1a\u70ed\u56fe\u7684\u7ed8\u5236\u4ee5\u53ca\u5206\u6790\u65b9\u6cd5\u4e86\u5417\uff1f\u540c\u5b66\u4eec\u4e5f\u53ef\u4ee5\u81ea\u884c\u4e0b\u8f7d\u4e00\u4e9b\u6570\u636e\uff0c\u7ed8\u5236\u5c5e\u4e8e\u4f60\u7684\u4e13\u5c5e\u201c\u8c03\u8272\u677f\u201d\uff01\u5927\u5bb6\u4e5f\u53ef\u4ee5\u79fb\u6b65\u4e91\u751f\u4fe1\u753b\u56fe\u4e13\u7248\u8fdb\u884c\u66f4\u6df1\u5165\u7684\u5b66\u4e60\u54e6\uff01<\/p>\n<p>\u5c0f\u679c\u4e91\u751f\u4fe1\u5e73\u53f0\u8868\u8fbe\u91cf\u70ed\u56fe\u7ed8\u5236\u5c0f\u5de5\u5177<a href=\"http:\/\/www.biocloudservice.com\/365\/365.php\">www.biocloudservice.com\/365\/365.php<\/a><\/p>\n<p>\u8d76\u7d27\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u5b66\u8d77\u6765\u5427\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u70ed\u56fe-\u751f\u6210\u4f60\u7684\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u201c\u8c03\u8272\u677f\u201d \u5f53\u6211\u4eec\u751f\u6210\u5355\u7ec6\u80de\u7684\u6570\u636e\u77e9\u9635\u5e76\u4e86\u89e3\u4e86\u7ec6\u80de\u4e2d\u57fa\u56e0\u8868\u8fbe\u7684\u57fa\u672c\u60c5\u51b5\u540e\uff0c\u6211\u4eec\u8981\u5982 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30174"}],"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=30174"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30174\/revisions"}],"predecessor-version":[{"id":30178,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30174\/revisions\/30178"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30174"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30174"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30174"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}