{"id":29446,"date":"2024-02-22T18:03:59","date_gmt":"2024-02-22T10:03:59","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29446"},"modified":"2024-02-22T18:04:01","modified_gmt":"2024-02-22T10:04:01","slug":"aucell%e8%af%86%e5%88%ab%e6%b4%bb%e6%80%a7%e5%9f%ba%e5%9b%a0%e9%9b%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29446","title":{"rendered":"AUCell\u201c\u8bc6\u522b\u201d\u6d3b\u6027\u57fa\u56e0\u96c6"},"content":{"rendered":"<p><strong>AUCell\u201c\u8bc6\u522b\u201d\u6d3b\u6027\u57fa\u56e0\u96c6<\/strong><\/p>\n<p>\u5404\u4f4d\u540c\u5b66\u4eec\uff01\u5c0f\u679c\u6280\u80fd\u8bfe\u5802\u7ec8\u4e8e\u53c8\u53cc\u7f00\u5f00\u8bfe\u5566\uff01\u4eca\u5929\u6211\u4eec\u8981\u5b66\u4e60\u4e00\u4e2a\u5168\u65b0\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u5de5\u5177\u6765\u89e3\u51b3\u4e00\u4e2a\u7279\u5b9a\u7684\u95ee\u9898\uff1a<\/p>\n<p>\u901a\u8fc7\u4ec0\u4e48\u6837\u7684\u65b9\u6cd5\u5c31\u80fd\u9274\u522b\u51fa\u7ec6\u80de\u4e2d\u5b58\u5728\u7684\u201c\u6d3b\u6027\u201d\u57fa\u56e0\u96c6\u5e76\u5c06\u5b83\u53ef\u89c6\u5316\u5c55\u793a\u5462\uff1f\u4e0d\u8981\u6025\uff0c\u5c0f\u679c\u5e26\u4f60\u4e00\u8d77\u63a2\u8ba8\uff01<\/p>\n<p><strong>AUCell\u5b89\u88c5<\/strong><\/p>\n<p>\u6ca1\u9519\uff0c\u6211\u4eec\u4eca\u5929\u8981\u7528\u5230\u7684\u5c31\u662fR\u5305&#8212;&#8211;AUCell\uff0cAUCell\u5177\u6709\u5f3a\u5927\u7684\u8bc6\u522b\u529f\u80fd\u548c\u7ed8\u56fe\u529f\u80fd\uff0c\u80fd\u591f\u8f7b\u677e\u89e3\u51b3\u6211\u4eec\u73b0\u5728\u60f3\u89e3\u51b3\u7684\u95ee\u9898\u54e6\u3002\u90a3\u5c31\u5148\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u5b8c\u6210AUCell\u5305\u7684\u5b89\u88c5\u5427\uff01<\/p>\n<p>BiocManager::install(&#8220;AUCell&#8221;,force = TRUE)<br \/>\n#\u672c\u6b21\u5b9e\u9a8c\u8fd8\u8981\u7528\u5230\u7684\u76f8\u5173\u4f9d\u8d56<br \/>\n#\u6211\u4eec\u9700\u8981\u7528GEOquery\u6765\u5bfc\u5165\u6211\u4eec\u540e\u7eed\u9700\u8981\u7528\u5230\u7684\u77e9\u9635\u6570\u636e<br \/>\nBiocManager::install(&#8220;GEOquery&#8221;,force = TRUE)<\/p>\n<p><strong>\u51c6\u5907\u6570\u636e<\/strong><\/p>\n<p>\u5728AUCell\u8fdb\u884c\u8bc6\u522b\u5e76\u8f93\u51fa\u4e4b\u524d\uff0c\u5c0f\u679c\u8981\u51c6\u5907\u6700\u57fa\u672c\u7684\u6570\u636e\uff0c\u5bf9\u4e8e\u672c\u6b21\u5b9e\u9a8c\uff0c\u6211\u4eec\u7528\u5230\u7684\u6570\u636e\u6709\u4e24\u79cd\uff0c\u4e00\u79cd\u662f\u201c\u77e9\u9635\u6570\u636e\u201d\uff0c\u4e00\u79cd\u662f\u201c\u57fa\u56e0\u6570\u636e\u201d\u54e6 \uff0c\u4f7f\u7528\u4e4b\u524d\u4e0b\u8f7d\u597d\u7684\u201cGEOquery\u201d\u5305\u5c31\u53ef\u4ee5\u76f4\u63a5\u5728R\u4e2d\u4e0b\u8f7dncbi\u4e0a\u7684\u6570\u636e\u96c6\u3002\u6211\u4eec\u5728\u4e0b\u8f7d\u597d\u540e\uff0c\u901a\u8fc7R\u4e2d\u5bf9\u6570\u636e\u5904\u7406\u7684\u51fd\u6570\u5c06\u5176\u8fdb\u884c\u4e8c\u6b21\u5c01\u88c5\uff0c\u4ece\u800c\u5c06\u5176\u8f6c\u5316\u4e3a\u6570\u636e\u77e9\u9635\u7684\u5f62\u5f0f~<\/p>\n<ul>\n<li><strong>\u51c6\u5907\u77e9\u9635\u6570\u636e<\/strong><\/li>\n<\/ul>\n<p>library(GEOquery)<br \/>\nlibrary(Matrix)<br \/>\ngsdata &lt;- getGEO(&#8216;GSE60361&#8217;) # does not work, the matrix is in a suppl file<br \/>\ngeo_file &lt;- &#8220;GSE60361_C1-3005-Expression.txt.gz&#8221;<br \/>\ndownload.file(&#8216;https:\/\/ftp.ncbi.nlm.nih.gov\/geo\/series\/GSE60nnn\/GSE60361\/suppl\/GSE60361_C1-3005-Expression.txt.gz&#8217;, destfile = geoFile)<br \/>\n\u200b<br \/>\n#\u6570\u636e\u5c01\u88c5<br \/>\neprMtrx &lt;- fread(geoFile, sep = &#8220;\\t&#8221;)<br \/>\ngen_name &lt;- unname(unlist(eprMtrx[, 1, with = FALSE]))<br \/>\neprMtrx &lt;- as.matrix(exprMatrix[, -1, with = FALSE])<br \/>\nrownames(eprMtrx) &lt;- gen_name<br \/>\nexprMatrix &lt;- exprMatrix[unique(rownames(exprMatrix)), ]<br \/>\ndim(exprMatrix)<br \/>\neprMtrx &lt;- as(eprMtrx, &#8220;dgCMatrix&#8221;)<br \/>\n\u200b<br \/>\n#\u6570\u636e\u4fdd\u5b58<br \/>\nmouseExprMatrix &lt;- eprMtrx<br \/>\nsave(mouseExprMatrix, file = &#8220;exprMatrix.RData&#8221;)<\/p>\n<ul>\n<li><strong>\u51c6\u5907\u57fa\u56e0\u6570\u636e<\/strong><\/li>\n<\/ul>\n<p>\u5bf9\u4e8e\u57fa\u56e0\u96c6\u6570\u636e\uff0c\u6211\u4eec\u53ef\u4ee5\u76f4\u63a5\u4eceAUCell\u8f6f\u4ef6\u5305\u4e2d\u81ea\u5e26\u7684\u6570\u636e\u96c6\u76f4\u63a5\u8c03\u53d6\uff0c\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\u5462\uff01\u8ba9\u5c0f\u679c\u5e26\u5927\u5bb6\u6765\u5177\u4f53\u770b\u770b\u600e\u4e48\u64cd\u4f5c\u5427\uff01<\/p>\n<p>library(AUCell)<br \/>\nlibrary(GSEABase)<br \/>\ngmtf &lt;- paste(file.path(system.file(&#8220;examples&#8221;, package = &#8220;AUCell&#8221;)), &#8220;geneSignatures.gmt&#8221;,<br \/>\nsep = &#8220;\/&#8221;)<br \/>\ngene-Sets &lt;- getGmt(gmtf)<br \/>\ngene-Sets &lt;- subsetGeneSets(gene-Sets, rownames(eprMtrx))<br \/>\ncbind(nGenes(gene-Sets))<br \/>\ngene-Sets &lt;- setGeneSetNames(gene-Sets, newNames = paste(names(geneSets), &#8221; (&#8220;, nGenes(geneSets),<br \/>\n&#8220;g)&#8221;, sep = &#8220;&#8221;))<br \/>\n\u200b<br \/>\nset.seed(321)<br \/>\nextraGeneSets &lt;- c(GeneSet(sample(rownames(exprMatrix), 50), setName = &#8220;Random (50g)&#8221;),<br \/>\nGeneSet(sample(rownames(exprMatrix), 500), setName = &#8220;Random (500g)&#8221;))<br \/>\n\u200b<br \/>\ncountsGene &lt;- apply(exprMatrix, 1, function(x) sum(x &gt; 0))<br \/>\n\u200b<br \/>\nextraSets &lt;- c(extraSets, GeneSet(sample(names(countsGene)[which(countsGene &gt;<br \/>\nquantile(countsGene, probs = 0.95))], 100), setName = &#8220;HK-like (100g)&#8221;))<br \/>\n\u200b<br \/>\ngene-Sets &lt;- GeneSetCollection(c(gene-Sets, extraSets))<br \/>\nnames(geneSets)<br \/>\n\u200b<br \/>\n\u200b<\/p>\n<ul>\n<li><strong>\u8bc6\u522b\u7ec6\u80de\u4e2d\u7684\u6d3b\u6027\u57fa\u56e0\u96c6<\/strong><\/li>\n<\/ul>\n<p>\u5f53AUCell\u8bc6\u522b\u4e86\u7ec6\u80de\u4e2d\u7684\u6d3b\u6027\u57fa\u56e0\u540e\uff0c\u4f1a\u6839\u636e\u6d3b\u6027\u57fa\u56e0\u5728\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u60c5\u51b5\u7528\u66f2\u9762\u9762\u79ef\u6765\u8fdb\u884c\u8868\u793a\u54e6\uff01\u8c03\u7528AUCell\u7684\u53ef\u89c6\u5316\u51fd\u6570\uff0c\u6211\u4eec\u4e5f\u53ef\u4ee5\u76f4\u89c2\u7684\u770b\u5230\u6570\u636e\u96c6\u4e2d\u7684\u7ec6\u80de\u4e2d\u8868\u8fbe\u51fa\u7684\u6d3b\u6027\u5f3a\u5ea6\uff0c\u4ece\u800c\u4e5f\u6709\u52a9\u4e8e\u6211\u4eec\u4ece\u6570\u636e\u7fa4\u4e2d\u627e\u5230\u6d3b\u6027\u5f3a\u7684\u4e00\u7cfb\u5217\u7ec6\u80de\uff01\u63a5\u4e0b\u6765\u5c0f\u679c\u5e26\u5927\u5bb6\u4e00\u8d77\u770b\u770bAUCell\u7684\u5f3a\u5927\u7ed8\u56fe\u529f\u80fd\u5427\uff01\uff01<\/p>\n<p>set.seed(120)<br \/>\npar(mfrow = c(3, 3))<br \/>\n#\u5c06\u77e9\u9635\u6570\u636e\u548c\u57fa\u56e0\u6570\u636e\u4f5c\u4e3a\u8f93\u5165<br \/>\ncells_AUC &lt;- AUCell_run(eprMtrx, gene-Sets)<br \/>\ncells &lt;- AUCell_exploreThresholds(cells_AUC, plotHist = TRUE, assign = TRUE)<\/p>\n<p>\u6765\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u770b\u8f93\u51fa\u7ed3\u679c\u5427\uff01\u6ce8\u610f\uff0c\u8fd9\u91cc\u56e0\u4e3a\u7ed8\u5236\u7684\u56fe\u5f88\u591a\uff0c\u6240\u4ee5\u6211\u4eec\u9700\u8981\u5c06\u53f3\u4e0b\u89d2\u7684\u56fe\u6846\u62c9\u5927\u4e00\u4e9b\u54e6\uff01\u4e0d\u7136\u53ef\u80fd\u4f1a\u5bfc\u81f4\u770b\u4e0d\u5230\u7ed8\u56fe\u7ed3\u679c\u54e6\uff01\uff01<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"373\" class=\"wp-image-29447\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=640%2C373\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?w=2500 2500w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=300%2C175 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=1024%2C597 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=768%2C448 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=1536%2C896 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=2048%2C1194 2048w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?resize=600%2C350 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?w=1280 1280w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/word-image-29446-1.png?w=1920 1920w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>D=====(\uffe3\u25bd\uffe3*)b========================<\/p>\n<p>\u597d\u5566\uff0c\u4eca\u5929\u8fd9\u4e2a\u6280\u80fd\u4f60\u6709\u597d\u597d\u8ddf\u5c0f\u679c\u4e00\u8d77\u5b66\u561b\uff1f\u4e0d\u77e5\u9053\u4f60\u5b66\u4f1a\u4e86\u6ca1\u6709\u634f\uff0c\u66f4\u591a\u5c0f\u6280\u80fd\u8bf7\u591a\u591a\u5173\u6ce8\u5c0f\u679c\u7684\u516c\u4f17\u53f7\u54e6\uff01\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"<p>AUCell\u201c\u8bc6\u522b\u201d\u6d3b\u6027\u57fa\u56e0\u96c6 \u5404\u4f4d\u540c\u5b66\u4eec\uff01\u5c0f\u679c\u6280\u80fd\u8bfe\u5802\u7ec8\u4e8e\u53c8\u53cc\u7f00\u5f00\u8bfe\u5566\uff01\u4eca\u5929\u6211\u4eec\u8981\u5b66\u4e60\u4e00\u4e2a\u5168\u65b0\u7684\u5355\u7ec6\u80de\u6d4b\u5e8f\u5de5 [&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\/29446"}],"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=29446"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29446\/revisions"}],"predecessor-version":[{"id":29448,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29446\/revisions\/29448"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29446"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29446"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29446"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}