{"id":757,"date":"2021-04-14T19:38:02","date_gmt":"2021-04-14T11:38:02","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=757"},"modified":"2021-04-14T21:35:54","modified_gmt":"2021-04-14T13:35:54","slug":"%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be%e8%b6%8b%e5%8a%bf%e5%88%86%e6%9e%90%ef%bc%88tcseq%e4%bd%bf%e7%94%a8%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=757","title":{"rendered":"\u57fa\u56e0\u8868\u8fbe\u8d8b\u52bf\u5206\u6790\uff08TCseq\u4f7f\u7528\uff09"},"content":{"rendered":"<p>TCseq\u53ef\u6839\u636e\u4e0d\u540c\u7684\u805a\u7c7b\u65b9\u6cd5\u5c06\u57fa\u56e0\u6309\u7167\u8868\u8fbe\u6a21\u5f0f\u5206\u7c7b<\/p>\n<pre>BiocManager::install(\"TCseq\")\nlibrary(TCseq)\ndata &lt;- read.delim('df_TCseq.xls', row.names = 1, sep = '\\t', check.names = FALSE)\ndata &lt;- as.matrix(data)\ntca &lt;- timeclust(data, algo = \"cm\", k = 6, standardize = TRUE)\n#character string giving a clustering method. Options are km' (kmeans), 'pam' (partitioning around medoids), 'hc' (hierachical clustering), 'cm' (cmeans).\np &lt;- timeclustplot(tca, value = \"z-score(TPM)\", cols = 3)#\u6240\u6709cluster\u5408\u5e76\u4e00\u4e2a\u56fe\nprint(p[[1]])#\u5355\u4e00cluster\u4f5c\u56fe\na &lt;- as.data.frame(tca@cluster)\ntable(a)\nnames(a) &lt;- 'Cluster'\nCluster2 &lt;- subset(a,Cluster == 2)\nwrite.table(Cluster2, file=\"Cluster2_gene.xls\", sep=\"\\t\", quote=F, row.names=T, col.names=T)\n<\/pre>\n<p>\u5bfc\u51fa\u4e0d\u540ccluster\u57fa\u56e0\u505a\u529f\u80fd\u5bcc\u96c6<\/p>\n","protected":false},"excerpt":{"rendered":"<p>TCseq\u53ef\u6839\u636e\u4e0d\u540c\u7684\u805a\u7c7b\u65b9\u6cd5\u5c06\u57fa\u56e0\u6309\u7167\u8868\u8fbe\u6a21\u5f0f\u5206\u7c7b BiocManager::install(&#8220;TCseq&#8221;) library(TCseq) data &lt;- read.delim(&#8216;df_TCseq.xls&#8217;, row.names = 1, sep = &#8216;\\t&#8217;, check.names = FALSE) data &lt;- as.matrix(data) tca &lt;- timeclust(data, algo = &#8220;cm&#8221;, k = 6, standardize = TRUE) #character string giving a clustering method. Options are km&#8217; (kmeans), &#8216;pam&#8217; (partitioning around medoids), &#8216;hc&#8217; (hierachical clustering), &#8216;cm&#8217; (cmeans). p &lt;- timeclustplot(tca, value = &#8220;z-score(TPM)&#8221;, [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/757"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=757"}],"version-history":[{"count":3,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/757\/revisions"}],"predecessor-version":[{"id":760,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/757\/revisions\/760"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=757"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=757"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=757"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}