{"id":16131,"date":"2023-10-23T10:16:25","date_gmt":"2023-10-23T02:16:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=16131"},"modified":"2023-10-23T10:16:26","modified_gmt":"2023-10-23T02:16:26","slug":"tadcompare%ef%bc%9a%e5%a4%a7%e6%b5%b7%e5%93%a5%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bc%9a%e6%8b%93%e6%89%91%e7%9b%b8%e5%85%b3%e5%9f%9f%e7%9a%84%e5%be%ae%e5%88%86%e5%92%8c%e6%97%b6%e9%97%b4%e5%88%86","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=16131","title":{"rendered":"TADCompare\uff1a\u5927\u6d77\u54e5\u624b\u628a\u624b\u6559\u4f1a\u62d3\u6251\u76f8\u5173\u57df\u7684\u5fae\u5206\u548c\u65f6\u95f4\u5206\u6790"},"content":{"rendered":"<p>\u5c0f\u4f19\u4f34\u4eec\u597d\u554a\uff01\u4e0d\u77e5\u9053\u5927\u5bb6\u6709\u6ca1\u6709\u5206\u6790\u62d3\u6251\u76f8\u5173\u57df\uff08Topologically Associated Domains\uff0cTAD\uff09\u7684\u9700\u6c42\u5462\u3002\u4eca\u5929\u5927\u6d77\u54e5\u5e26\u6765\u4e86<a id=\"post-16131-OLE_LINK1\"><\/a><a id=\"post-16131-OLE_LINK2\"><\/a>TADCompare\uff0c\u5b83\u529f\u80fd\u6781\u5176\u5f3a\u5927\u3002\u63a5\u4e0b\u6765\uff0c\u8ddf\u7740\u5927\u6d77\u54e5\u8ba4\u8bc6\u548c\u5b66\u4f1a\u4f7f\u7528TADCompare\u5427\uff01<\/p>\n<p><strong>1 \u4ecb\u7ecd<\/strong><\/p>\n<p>\u8fd1\u671f\u7684\u7814\u7a76\u5229\u7528\u67d3\u8272\u8d28\u6784\u8c61\u6355\u83b7\u6280\u672f\uff0c\u5982Hi-C\uff0c\u5df2\u7ecf\u8bc1\u660e\u4e86\u62d3\u6251\u5173\u8054\u57df\uff08TADs\uff09\u548c\u8f83\u5c0f\u7684\u67d3\u8272\u8d28\u73af\uff0c\u5728\u6b64\u7edf\u79f0\u4e3a\u201c\u4ea4\u4e92\u57df\u201d\u7684\u91cd\u8981\u6027\u3002\u8bb8\u591a\u8fd9\u6837\u7684\u57df\u5728\u53d1\u80b2\u6216\u75be\u75c5\u8fc7\u7a0b\u4e2d\u53d1\u751f\u53d8\u5316\uff0c\u5e76\u8868\u73b0\u51fa\u7ec6\u80de\u548c\u6761\u4ef6\u7279\u5f02\u6027\u5dee\u5f02\u3002\u5bf9\u4ea4\u4e92\u57df\u52a8\u6001\u884c\u4e3a\u8fdb\u884c\u91cf\u5316\u5c06\u6709\u52a9\u4e8e\u66f4\u597d\u5730\u7406\u89e3\u57fa\u56e0\u7ec4\u8c03\u63a7\u3002\u6bd4\u8f83\u4e0d\u540c\u7ec6\u80de\u548c\u6761\u4ef6\u4e0b\u7684\u4ea4\u4e92\u57df\u7684\u65b9\u6cd5\u975e\u5e38\u6709\u9650\u3002<\/p>\n<p>\u636e\u6211\u4eec\u6240\u77e5\uff0c\u76ee\u524d\u53ea\u6709\u4e09\u79cd\u65b9\u6cd5\u53ef\u4ee5\u9002\u5e94\u68c0\u6d4b\u76f8\u4e92\u4f5c\u7528\u57df\u8fb9\u754c\u7684\u53d8\u5316\uff1b\u5176\u4e2d\u5927\u591a\u6570\u662f\u4e3a\u68c0\u6d4b\u7279\u5b9a\u4e8eTAD\u7684\u8fb9\u754c\u53d8\u5316\u800c\u5f00\u53d1\u7684\u3002\u5728\u8fd9\u4e09\u79cd\u65b9\u6cd5\u4e2d\uff0clocaltadsim\u3001HiCDB\u548cDiffTAD\uff0c\u6ca1\u6709\u4e00\u4e2a\u63d0\u4f9b\u76f4\u89c2\u3001\u6613\u4e8e\u4f7f\u7528\u7684\u65b9\u5f0f\u6765\u8c03\u7528\u5dee\u5f02\u8fb9\u754c\u3002localtadsim\u548cDiffTAD\u90fd\u662f\u4e24\u6b65\u7a0b\u5e8f\uff0c\u9700\u8981\u5206\u522b\u5b9a\u4e49TADs\u5e76\u901a\u8fc7\u547d\u4ee4\u884c\u5b9e\u7528\u7a0b\u5e8f\u8fdb\u884c\u6bd4\u8f83\u3002HiCDB\u6709\u4e00\u4e2a\u5185\u7f6e\u7684TAD\u8c03\u7528\u5668\uff0c\u4f46\u4e0d\u5141\u8bb8\u5bf9\u67d3\u8272\u4f53\u7279\u5f02\u6027\u63a5\u89e6\u77e9\u9635\u8fdb\u884c\u6bd4\u8f83\u3002\u6240\u6709\u8fd9\u4e09\u79cd\u65b9\u6cd5\u90fd\u9700\u8981\u9ad8\u5ea6\u7279\u5b9a\u7684\u6570\u636e\u7c7b\u578b\u548c\u6587\u4ef6\u540d\u624d\u80fd\u8fd0\u884c\u3002\u7f3a\u4e4f\u53ef\u7528\u6027\u7684\u95ee\u9898\u4e0e\u8bf8\u5982\u7f3a\u4e4f\u7ef4\u62a4\u3001\u8fd0\u884c\u7f13\u6162\u548c\u7f3a\u4e4f\u7edf\u8ba1\u4e25\u8c28\u6027\u7b49\u95ee\u9898\u76f8\u7ed3\u5408\u3002<\/p>\n<p>\u4f5c\u8005\u5f00\u53d1\u4e86TADCompare\uff0c\u8fd9\u662f\u4e00\u4e2aR\u5305\uff0c\u65e8\u5728\u63d0\u4f9b\u4e00\u4e2a\u5feb\u901f\u3001\u51c6\u786e\u3001\u7528\u6237\u53cb\u597d\u4e14\u8bb0\u5f55\u5b8c\u5584\u7684TAD\u548c\u67d3\u8272\u8d28\u73af\u8def\u8fb9\u754c\u5dee\u5f02\u5206\u6790\u65b9\u6cd5\u3002\u4ed6\u4eec\u5f15\u5165\u4e86\u4e00\u79cd\u57fa\u4e8e\u8fb9\u754c\u5f97\u5206\u7edf\u8ba1\u91cf\u7684\u65b9\u6cd5\uff0c\u5e76\u7528\u5b83\u6765\u8bc6\u522b\u4e94\u79cd\u7c7b\u578b\u7684\u8fb9\u754c\u53d8\u5316\u3002\u8be5\u65b9\u6cd5\u88ab\u6269\u5c55\u4ee5\u5141\u8bb8\u8c03\u7528\u5171\u8bc6\u8fb9\u754c\u5e76\u5728Hi-C\u91cd\u590d\u7ec4\u4e4b\u95f4\u8fdb\u884c\u6bd4\u8f83\u3002\u4ed6\u4eec\u8fd8\u5c55\u793a\u4e86\u5982\u4f55\u4f7f\u7528\u8fb9\u754c\u5f97\u5206\u7edf\u8ba1\u91cf\u6765\u5206\u6790\u76f8\u4e92\u4f5c\u7528\u57df\u8fb9\u754c\u968f\u65f6\u95f4\u7684\u53d8\u5316\u52a8\u6001\u3002\u5bf9\u4e8e\u5dee\u5f02\u8fb9\u754c\u68c0\u6d4b\u548c\u65f6\u95f4\u5e8f\u5217\u5206\u6790\uff0c\u4ed6\u4eec\u63d0\u4f9b\u4e86\u7528\u4e8e\u5206\u7c7b\u8fb9\u754c\u53d8\u5316\u7684\u65b0\u9896\u672f\u8bed\u3002\u4ed6\u4eec\u4f7f\u7528\u5177\u6709\u9884\u5b9a\u4e49\u4ea4\u4e92\u4f5c\u7528\u57df\u7684\u6a21\u62df\u6570\u636e\u6f14\u793a\u4e86TADCompare\u7684\u9c81\u68d2\u6027\u4ee5\u53ca\u5176\u63ed\u793a\u4e0d\u540c\u8fb9\u754c\u53d8\u5316\u7684\u4e0d\u540c\u751f\u7269\u5b66\u89d2\u8272\u7684\u80fd\u529b\u3002\u603b\u4e4b\uff0cTADCompare\u63d0\u4f9b\u4e86\u4e00\u4e2a\u4ece\u5171\u8bc6\u8fb9\u754c\u8c03\u7528\u5230\u5dee\u5f02\u8fb9\u754c\u68c0\u6d4b\u7684\u4e00\u7ad9\u5f0f\u7ba1\u9053\uff0c\u5305\u62ec\u65f6\u95f4\u5e8f\u5217\u5206\u6790\u3002\u8f93\u51fa\u4ee5\u5e38\u7528\u7684BED\u683c\u5f0f\u683c\u5f0f\u5316\uff0c\u5141\u8bb8\u7075\u6d3b\u7684\u4e0b\u6e38\u5206\u6790\u548c\u53ef\u89c6\u5316\u3002<\/p>\n<p><strong>2 \u529f\u80fd<\/strong><\/p>\n<p>TimeCompare\u662f\u4e00\u4e2aR\u8bed\u8a00\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u6bd4\u8f83\u4e0d\u540c\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u4e4b\u95f4\u7684\u76f8\u4f3c\u6027\u3002\u8fd9\u4e2a\u5305\u63d0\u4f9b\u4e86\u591a\u79cd\u65b9\u6cd5\u6765\u5ea6\u91cf\u548c\u6bd4\u8f83\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u7684\u76f8\u4f3c\u6027\uff0c\u5305\u62ec\u52a8\u6001\u65f6\u95f4\u89c4\u6574\uff08DTW\uff09\u3001\u6700\u957f\u516c\u5171\u5b50\u5e8f\u5217\uff08LCSS\uff09\u7b49\u3002\u5176\u4e3b\u8981\u529f\u80fd\u5305\u62ec\uff1a<\/p>\n<ul>\n<li>\u8ba1\u7b97\u4e24\u4e2a\u65f6\u95f4\u5e8f\u5217\u4e4b\u95f4\u7684\u76f8\u4f3c\u5ea6\uff1a\u901a\u8fc7\u4f7f\u7528\u4e0d\u540c\u7684\u76f8\u4f3c\u5ea6\u5ea6\u91cf\u65b9\u6cd5\uff0c\u53ef\u4ee5\u8ba1\u7b97\u51fa\u4e24\u4e2a\u65f6\u95f4\u5e8f\u5217\u4e4b\u95f4\u7684\u76f8\u4f3c\u5ea6\u3002\u8fd9\u4e9b\u65b9\u6cd5\u5305\u62ecDTW\u3001LCSS\u3001\u6b27\u6c0f\u8ddd\u79bb\u7b49\u3002<\/li>\n<li>\u53ef\u89c6\u5316\u65f6\u95f4\u5e8f\u5217\u6570\u636e\uff1aTimeCompare\u5305\u63d0\u4f9b\u4e86\u591a\u79cd\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u53ef\u4ee5\u5e2e\u52a9\u7528\u6237\u66f4\u597d\u5730\u7406\u89e3\u548c\u5206\u6790\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u3002\u8fd9\u4e9b\u5de5\u5177\u5305\u62ec\u65f6\u5e8f\u56fe\u3001\u6563\u70b9\u56fe\u7b49\u3002<\/li>\n<li>\u63d0\u4f9b\u591a\u79cd\u76f8\u4f3c\u5ea6\u5ea6\u91cf\u65b9\u6cd5\uff1a\u9664\u4e86DTW\u3001LCSS\u3001\u6b27\u6c0f\u8ddd\u79bb\u7b49\u5e38\u89c1\u7684\u76f8\u4f3c\u5ea6\u5ea6\u91cf\u65b9\u6cd5\u5916\uff0cTimeCompare\u5305\u8fd8\u63d0\u4f9b\u4e86\u5176\u4ed6\u4e00\u4e9b\u7279\u6b8a\u7684\u76f8\u4f3c\u5ea6\u5ea6\u91cf\u65b9\u6cd5\uff0c\u5982\u52a8\u6001\u65f6\u95f4\u89c4\u6574\u52a0\u6743\uff08DTW-Weighted\uff09\u3001\u52a8\u6001\u65f6\u95f4\u89c4\u6574\u52a0\u6743\u5e73\u5747\uff08DTW-Weighted Average\uff09\u7b49\u3002<\/li>\n<li>\u652f\u6301\u591a\u79cd\u6570\u636e\u7c7b\u578b\uff1aTimeCompare\u5305\u4e0d\u4ec5\u53ef\u4ee5\u5904\u7406\u8fde\u7eed\u7684\u65f6\u95f4\u5e8f\u5217\u6570\u636e\uff0c\u8fd8\u53ef\u4ee5\u5904\u7406\u79bb\u6563\u7684\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u3002\u6b64\u5916\uff0c\u5b83\u8fd8\u53ef\u4ee5\u5904\u7406\u6df7\u5408\u7c7b\u578b\u7684\u65f6\u95f4\u5e8f\u5217\u6570\u636e\uff0c\u5373\u5305\u542b\u8fde\u7eed\u548c\u79bb\u6563\u4e24\u79cd\u7c7b\u578b\u7684\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u3002<\/li>\n<\/ul>\n<p><strong>3 \u5b89\u88c5<\/strong><\/p>\n<p>\u9700\u8981\u5b89\u88c5\u7684\u5305\u6709\u4e9b\u591a\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u76f4\u63a5\u4f7f\u7528\u5927\u6d77\u54e5\u5199\u597d\u7684\u4ee3\u7801\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td><a id=\"post-16131-_Hlk148652289\"><\/a> install.packages(c(&#8216;dplyr&#8217;, &#8216;PRIMME&#8217;, &#8216;cluster&#8217;, &#8216;Matrix&#8217;, &#8216;magrittr&#8217;, &#8216;HiCcompare&#8217;))<\/p>\n<p>if (!requireNamespace(&#8220;BiocManager&#8221;, quietly=TRUE))<\/p>\n<p>install.packages(&#8220;BiocManager&#8221;)<\/p>\n<p>BiocManager::install(&#8220;TADCompare&#8221;, version = &#8220;devel&#8221;)<\/p>\n<p>BiocManager::install(&#8216;SpectralTAD&#8217;)<\/p>\n<p>library(TADCompare)<\/p>\n<p># Or, for the developmental version<\/p>\n<p>#devtools::install_github(&#8220;dozmorovlab\/TADCompare&#8221;)<\/p>\n<p>library(dplyr)<\/p>\n<p>library(PRIMME)<\/p>\n<p>library(cluster)<\/p>\n<p>library(Matrix)<\/p>\n<p>library(magrittr)<\/p>\n<p>library(HiCcompare)<\/p>\n<p>library(SpectralTAD)<\/p>\n<p>library(TADCompare)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>4 TADCompare<\/strong><\/p>\n<p><strong>4.1 \u4ecb\u7ecd<\/strong><\/p>\n<p>TADCompare\u662f\u4e00\u4e2a\u51fd\u6570\uff0c\u5b83\u5141\u8bb8\u7528\u6237\u81ea\u52a8\u8bc6\u522b\u4e24\u4e2a\u6570\u636e\u96c6\u4e4b\u95f4\u7684\u5dee\u5f02\u6027TAD\u8fb9\u754c\u3002\u5bf9\u4e8e\u6bcf\u4e2a\u5dee\u5f02\u6027\u8fb9\u754c\uff0c\u8be5\u5305\u63d0\u4f9b\u4e86\u72ec\u7279\u7684\u5206\u7c7b\uff08\u590d\u6742\u3001\u5408\u5e76\u3001\u5206\u5272\u3001\u79fb\u52a8\u548c\u5f3a\u5ea6\u53d8\u5316\uff09\uff0c\u5b9a\u4e49\u4e86TAD\u8fb9\u754c\u5728\u6570\u636e\u96c6\u4e4b\u95f4\u7684\u53d8\u5316\u65b9\u5f0f\u3002<\/p>\n<p><strong>4.2 \u8fd0\u884c<\/strong><\/p>\n<p>\u552f\u4e00\u9700\u8981\u8f93\u5165\u7684\u662f\u4e24\u4e2a\u63a5\u89e6\u77e9\u9635\uff0c\u5b83\u4eec\u9700\u8981\u7b26\u5408\u5728\u201c\u8f93\u5165\u6570\u636e\u201d\u5c0f\u8282\uff08<a href=\"https:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/TADCompare\/inst\/doc\/Input_Data.html\">https:\/\/bioconductor.org\/packages\/release\/bioc\/vignettes\/TADCompare\/inst\/doc\/Input_Data.html<\/a>\uff09\u4e2d\u6307\u5b9a\u7684\u5141\u8bb8\u683c\u5f0f\u4e4b\u4e00\u3002TADCompare\u51fd\u6570\u5c06\u81ea\u52a8\u786e\u5b9a\u77e9\u9635\u7684\u7c7b\u578b\u5e76\u5c06\u5176\u8f6c\u6362\u4e3a\u9002\u5f53\u7684\u683c\u5f0f\uff0c\u53ea\u8981\u5b83\u662f\u652f\u6301\u7684\u683c\u5f0f\u4e4b\u4e00\u5373\u53ef\u3002\u552f\u4e00\u7684\u8981\u6c42\u662f\u6240\u6709\u77e9\u9635\u90fd\u91c7\u7528\u76f8\u540c\u7684\u683c\u5f0f\u3002\u4e3a\u4e86\u83b7\u5f97\u6700\u5feb\u7684\u7ed3\u679c\uff0c\u5927\u6d77\u54e5\u5efa\u8bae\u4f7f\u7528<strong>n\u00d7n<\/strong>\u7684\u77e9\u9635\u3002\u6b64\u5916\uff0c\u5efa\u8bae\u5c0f\u4f19\u4f34\u4eec\u63d0\u4f9b\u81ea\u5df1\u6570\u636e\u7684\u5206\u8fa8\u7387\u3002\u5982\u679c\u672a\u63d0\u4f9b\u5206\u8fa8\u7387\uff0c\u8be5\u5305\u5c06\u4f7f\u7528\u63a5\u89e6\u77e9\u9635\u7684\u6570\u5b57\u5217\u540d\u8fdb\u884c\u4f30\u8ba1\u3002\u5927\u6d77\u54e5\u5c06\u4f7f\u7528\u6765\u81eaGM12878\u7ec6\u80de\u7cfb\u3001\u67d3\u8272\u4f5322\u300150kb\u5206\u8fa8\u7387\u7684\u6570\u636e\u6765\u6f14\u793a\u8fd0\u884cTADCompare\u7684\u8fc7\u7a0b\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u83b7\u53d6\u5305\u5185\u6784\u5efa\u7684RAO\u63a5\u89e6\u77e9\u9635\u3002<\/p>\n<p>data(&#8220;rao_chr22_prim&#8221;)<\/p>\n<p>data(&#8220;rao_chr22_rep&#8221;)<\/p>\n<p>#\u6211\u4eec\u53ef\u4ee5\u770b\u5230\uff0c\u8fd9\u4e9b\u90fd\u662fn x n\u7684\u77e9\u9635\u3002<\/p>\n<p>dim(rao_chr22_prim)<\/p>\n<p>## [1] 704 704<\/p>\n<p>dim(rao_chr22_rep)<\/p>\n<p>## [1] 704 704<\/p>\n<p>#\u7b80\u5355\u67e5\u770b\u6570\u636e<\/p>\n<p>rao_chr22_prim[100:105, 100:105]<\/p>\n<p>## 2.1e+07 21050000 21100000 21150000 21200000 21250000<\/p>\n<p>## 2.1e+07 6215 1047 1073 714 458 383<\/p>\n<p>## 21050000 1047 4542 2640 1236 619 489<\/p>\n<p>## 21100000 1073 2640 13468 4680 1893 1266<\/p>\n<p>## 21150000 714 1236 4680 13600 4430 2124<\/p>\n<p>## 21200000 458 619 1893 4430 11313 4465<\/p>\n<p>## 21250000 383 489 1266 2124 4465 11824<\/p>\n<p>#\u8fd0\u884c\u6307\u5b9a\u5206\u8fa8\u7387\u7684\u7b97\u6cd5<\/p>\n<p>results = TADCompare(rao_chr22_prim, rao_chr22_rep, resolution = 50000)<\/p>\n<p>#\u5728\u6ca1\u6709\u6307\u5b9a\u5206\u8fa8\u7387\u7684\u60c5\u51b5\u4e0b\u91cd\u590d<\/p>\n<p>no_res = TADCompare(rao_chr22_prim, rao_chr22_rep)<\/p>\n<p>## Estimating resolution<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>4.3 TAD\u7684\u7c7b\u578b\u6bd4\u8f83\u8f93\u51fa<\/strong><\/p>\n<p>TADCompare\u51fd\u6570\u8fd4\u56de\u4e00\u4e2a\u5217\u8868\uff0c\u5176\u4e2d\u5305\u542b\u4e24\u4e2a\u6570\u636e\u6846\u548c\u4e00\u4e2a\u56fe\u3002\u7b2c\u4e00\u4e2a\u6570\u636e\u6846\u5305\u542b\u5728\u81f3\u5c11\u4e00\u4e2a\u63a5\u89e6\u77e9\u9635\u4e2d\u5305\u542bTAD\u8fb9\u754c\u7684\u57fa\u56e0\u7ec4\u7684\u6240\u6709\u533a\u57df\u3002\u7ed3\u679c\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>head(results$TAD_Frame)<\/p>\n<p>## Boundary Gap_Score TAD_Score1 TAD_Score2 Differential Enriched_In<\/p>\n<p>## 1 16300000 -18.6589859 0.7698503 7.704411 Differential Matrix 2<\/p>\n<p>## 2 16850000 0.2361100 7.8431724 7.580056 Non-Differential Matrix 1<\/p>\n<p>## 3 17350000 0.9683905 3.6628411 3.220253 Non-Differential Matrix 1<\/p>\n<p>## 4 18000000 -0.1033894 2.3616107 2.347392 Non-Differential Matrix 2<\/p>\n<p>## 5 18750000 3.0426660 4.7997622 3.558975 Differential Matrix 1<\/p>\n<p>## 6 18850000 2.6911660 3.7674844 2.680707 Differential Matrix 1<\/p>\n<p>## Type<\/p>\n<p>## 1 &lt;NA&gt;<\/p>\n<p>## 2 Non-Differential<\/p>\n<p>## 3 Non-Differential<\/p>\n<p>## 4 Non-Differential<\/p>\n<p>## 5 Strength Change<\/p>\n<p>## 6 Strength Change<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u201cBoundary\u201d\u5217\u5305\u542b\u7ed9\u5b9a\u8fb9\u754c\u7684\u57fa\u56e0\u7ec4\u5750\u6807\u3002\u201cGap_Score\u201d\u5bf9\u5e94\u4e8e\u5dee\u5f02\u8fb9\u754c\u5f97\u5206\uff08\u8fb9\u754c\u5f97\u5206\u4e4b\u95f4\u7684\u5dee\u503c\u7684Z\u5206\u6570\uff09\u3002\u201cTAD_Score1\u201d\u548c\u201cTAD_Score2\u201d\u5bf9\u5e94\u4e8e\u4e24\u4e2a\u63a5\u89e6\u77e9\u9635\u7684\u8fb9\u754c\u5f97\u5206\u3002\u201cDifferential\u201d\u7b80\u5355\u5730\u8868\u793a\u8fb9\u754c\u662f\u5426\u5177\u6709\u5dee\u5f02\u6027\u3002\u201cEnriched_In\u201d\u6307\u793a\u54ea\u4e2a\u77e9\u9635\u5305\u542bTAD\u8fb9\u754c\u3002\u201cType\u201d\u6807\u8bc6TAD\u8fb9\u754c\u53d8\u5316\u7684\u7c7b\u578b\u3002\u6ce8\u610f\uff1a\u7531\u4e8e\u6ca1\u6709\u5de6\u53f3\u53c2\u8003\u8fb9\u754c\uff0c\u7b2c\u4e00\u4e2a\u8fb9\u754c\u59cb\u7ec8\u88ab\u5f52\u7c7b\u4e3a\u201cNA\u201d\u3002<\/p>\n<p>\u7b2c\u4e8c\u4e2a\u6570\u636e\u6846\u5305\u542b\u4e0e\u7b2c\u4e00\u4e2a\u6570\u636e\u6846\u76f8\u540c\u7684\u4fe1\u606f\uff0c\u4f46\u5305\u62ec\u57fa\u56e0\u7ec4\u7684\u6bcf\u4e00\u4e2a\u533a\u57df\u3002\u6211\u4eec\u5728\u4e0b\u9762\u5c55\u793a\u5b83\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>head(results$Boundary_Scores)<\/p>\n<p>## Boundary TAD_Score1 TAD_Score2 Gap_Score Differential Enriched_In<\/p>\n<p>## 1 16300000 0.7698503 7.7044114 -18.658985912 Differential Matrix 2<\/p>\n<p>## 2 16850000 7.8431724 7.5800558 0.236110024 Non-Differential Matrix 1<\/p>\n<p>## 3 16900000 -0.4402121 -0.4337948 0.009161239 Non-Differential Matrix 1<\/p>\n<p>## 4 16950000 -0.7460531 -0.5551327 -0.467725582 Non-Differential Matrix 2<\/p>\n<p>## 5 17000000 -0.6803509 -0.6512025 -0.037456910 Non-Differential Matrix 2<\/p>\n<p>## 6 17050000 -0.6626352 -0.5562997 -0.245694062 Non-Differential Matrix 2<\/p>\n<p>## Type<\/p>\n<p>## 1 &lt;NA&gt;<\/p>\n<p>## 2 Non-Differential<\/p>\n<p>## 3 Non-Differential<\/p>\n<p>## 4 Non-Differential<\/p>\n<p>## 5 Non-Differential<\/p>\n<p>## 6 Non-Differential<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u6700\u540e\uff0c\u8fd8\u6709\u4e00\u4e2a\u5305\u542b\u5806\u53e0\u6761\u5f62\u56fe\u7684\u56fe\uff0c\u8be5\u56fe\u663e\u793a\u4e86\u6bcf\u79cd\u7c7b\u578b\u7684TAD\u8fb9\u754c\u7684\u6d41\u884c\u7a0b\u5ea6\u3002\u6761\u5f62\u56fe\u662f\u4e00\u4e2aggplot2\u5bf9\u8c61\uff0c\u56e0\u6b64\u5b8c\u5168\u53ef\u5b9a\u5236\u3002\u6211\u4eec\u5728\u4e0b\u9762\u5c55\u793a\u4e86\u8fd9\u4e2a\u56fe\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>p &lt;- results$Count_Plot<\/p>\n<p>class(p)<\/p>\n<p>## [1] &#8220;gg&#8221; &#8220;ggplot&#8221;<\/p>\n<p>plot(p)<\/p>\n<p>## Warning: Removed 1 rows containing missing values (`position_stack()`).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"1089\" height=\"775\" class=\"wp-image-16132\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1.png\" srcset=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1.png 1089w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1-300x213.png 300w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1-1024x729.png 1024w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1-768x547.png 768w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-1-600x427.png 600w\" sizes=\"(max-width: 1089px) 100vw, 1089px\" \/><\/p>\n<p><strong>4.4 \u9884\u5148\u89c4\u5b9a\u7684\u8f6c\u5f55\u8c03\u63a7\u533a\u57df<\/strong><\/p>\n<p>\u6211\u4eec\u8ba4\u8bc6\u5230\uff0c\u7528\u6237\u53ef\u80fd\u5e0c\u671b\u5728\u8fb9\u754c\u6bd4\u8f83\u4e4b\u524d\u4f7f\u7528\u81ea\u5df1\u7684TAD\u8c03\u7528\u5668\u6765\u8bc6\u522bTAD\u8fb9\u754c\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u63d0\u4f9b\u4e86\u4e00\u79cd\u9884\u5148\u89c4\u5b9aTAD\u7684\u9009\u9879\uff0c\u4ee5\u4e24\u4e2a\u6570\u636e\u6846\u7684\u5f62\u5f0f\uff0c\u5305\u542b\u4e24\u79cd\u63a5\u89e6\u77e9\u9635\u7684TAD\u8fb9\u754c\u7684\u67d3\u8272\u4f53\u3001\u8d77\u59cb\u548c\u7ed3\u675f\u5750\u6807\u3002\u901a\u8fc7\u8fd9\u4e2a\u9009\u9879\uff0c\u53ea\u6709\u63d0\u4f9b\u7684TAD\u8fb9\u754c\u5c06\u88ab\u6d4b\u8bd5\u3002\u5927\u6d77\u54e5\u5728\u8fd9\u63d0\u4f9b\u4e00\u4e2a\u4f7f\u7528SpectralTAD TAD\u8c03\u7528\u5668\u7684\u793a\u4f8b\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u8c03\u7528SpectralTAD\u8fdb\u884c\u62d3\u6251\u5173\u8054\u57df\u5206\u6790<\/p>\n<p>bed_coords1 = bind_rows(SpectralTAD::SpectralTAD(rao_chr22_prim, chr = &#8220;chr22&#8221;, levels = 3))<\/p>\n<p>## Estimating resolution<\/p>\n<p>bed_coords2 = bind_rows(SpectralTAD(rao_chr22_rep, chr = &#8220;chr22&#8221;, levels = 3))<\/p>\n<p>## Estimating resolution<\/p>\n<p>#\u5c06\u63a5\u89e6\u77e9\u9635\u7684TAD\u8fb9\u754c\u8fdb\u884c\u7ec4\u5408<\/p>\n<p>Combined_Bed = list(bed_coords1, bed_coords2)<\/p>\n<p>#\u6253\u5370\u7ec4\u5408\u7684TAD\u8fb9\u754c\u5217\u8868<\/p>\n<p>Combined_Bed[1]<\/p>\n<p>##[[1]]<\/p>\n<p>## A tibble: 261 \u00d7 4<\/p>\n<p>## chr start end Level<\/p>\n<p>## &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;<\/p>\n<p>## 1 chr2 8000000 8480000 1<\/p>\n<p>## 2 chr2 8480000 8880000 1<\/p>\n<p>## 3 chr2 8880000 9600000 1<\/p>\n<p>## 4 chr2 9600000 10240000 1<\/p>\n<p>## 5 chr2 10240000 10880000 1<\/p>\n<p>## 6 chr2 10880000 11320000 1<\/p>\n<p>## 7 chr2 11320000 12000000 1<\/p>\n<p>## 8 chr2 12000000 12320000 1<\/p>\n<p>## 9 chr2 12320000 12920000 1<\/p>\n<p>##10 chr2 12920000 13320000 1<\/p>\n<p>## \u2139 251 more rows<\/p>\n<p>## \u2139 Use `print(n = &#8230;)` to see more rows<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u5728\u4e0a\u9762\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230SpectralTAD\u8f93\u51fa\u7684\u6570\u636e\u96c6\u5305\u542b\u540d\u4e3a\u201cstart\u201d\u548c\u201cend\u201d\u7684\u5217\uff0c\u5206\u522b\u8868\u793a\u6bcf\u4e2aTAD\u7684\u8d77\u59cb\u548c\u7ed3\u675f\u5750\u6807\u3002\u8fd9\u662f\u5fc5\u9700\u7684\uff0c\u5c3d\u7ba1\u4efb\u4f55TAD\u8c03\u7528\u5668\u7684\u8f93\u51fa\u90fd\u53ef\u4ee5\u6709\u6548\u5730\u4e0e\u4e00\u4e9b\u6570\u636e\u64cd\u4f5c\u4e00\u8d77\u4f7f\u7528\u3002 \u201cLevel\u201d\u5217\u8868\u793aTAD\u5728\u5c42\u6b21\u7ed3\u6784\u4e2d\u7684\u7ea7\u522b\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u7528\u9884\u5148\u89c4\u5b9a\u7684TADs\u8fd0\u884cTADCompare<\/p>\n<p>TD_Compare = TADCompare(rao_chr22_prim, rao_chr22_rep, resolution = 50000, pre_tads = Combined_Bed)<\/p>\n<p>#\u8fd4\u56de\u8fb9\u754c<\/p>\n<p>head(TD_Compare$TAD_Frame)<\/p>\n<p>## Boundary Gap_Score TAD_Score1 TAD_Score2 Differential Enriched_In<\/p>\n<p>## 1 16850000 0.23611002 7.8431724 7.5800558 Non-Differential Matrix 1<\/p>\n<p>## 2 17250000 -0.08875306 0.1103987 0.1409999 Non-Differential Matrix 2<\/p>\n<p>## 3 17300000 -0.12694247 -0.6160007 -0.5549497 Non-Differential Matrix 2<\/p>\n<p>## 4 17350000 0.96839048 3.6628411 3.2202526 Non-Differential Matrix 1<\/p>\n<p>## 5 17600000 -0.06733403 -0.4153272 -0.3809658 Non-Differential Matrix 2<\/p>\n<p>## 6 18000000 -0.10338944 2.3616107 2.3473922 Non-Differential Matrix 2<\/p>\n<p>## Type<\/p>\n<p>## 1 Non-Overlap<\/p>\n<p>## 2 Non-Overlap<\/p>\n<p>## 3 Non-Overlap<\/p>\n<p>## 4 Non-Overlap<\/p>\n<p>## 5 Non-Overlap<\/p>\n<p>## 6 Non-Differential<\/p>\n<p>#\u8fdb\u884c\u6d4b\u8bd5\u6765\u663e\u793a\u6240\u6709\u9884\u5148\u89c4\u5b9a\u7684\u8fb9\u754c\u90fd\u88ab\u8fd4\u56de\u4e86<\/p>\n<p>table(TD_Compare$TAD_Frame$Boundary %in% bind_rows(Combined_Bed)$end)<\/p>\n<p>##<\/p>\n<p>## TRUE<\/p>\n<p>## 96<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u8fd4\u56de\u7684\u8fb9\u754c\u4ec5\u9650\u4e8e\u6211\u4eec\u9884\u5148\u89c4\u5b9a\u7684\u90a3\u4e9b\u3002<\/p>\n<p><strong>4.5 TADCompare\u7ed3\u679c\u7684\u53ef\u89c6\u5316<\/strong><\/p>\n<p>\u6211\u4eec\u63d0\u4f9b\u4e86\u4f7f\u7528DiffPlot\u51fd\u6570\u53ef\u89c6\u5316\u5dee\u5f02\u6027TAD\u8fb9\u754c\u7684\u65b9\u6cd5\u3002\u4f5c\u4e3a\u8f93\u5165\uff0cDiffPlot\u63a5\u53d7\u6765\u81eaTADCompare\u51fd\u6570\u548c\u539f\u59cb\u63a5\u89e6\u77e9\u9635\u7684\u8f93\u51fa\u3002\u4f5c\u4e3a\u8f93\u51fa\uff0c\u5b83\u8fd4\u56de\u4e00\u4e2a\u53ef\u4ee5\u8fdb\u4e00\u6b65\u5b9a\u5236\u7684ggplot2\u5bf9\u8c61\u3002\u6211\u4eec\u6f14\u793a\u4e86\u5728\u67d3\u8272\u4f532\u7684\u5b50\u96c6\u4e0a\uff0c\u4ee540kb\u5206\u8fa8\u7387\u5904\u7406\u7684\u6570\u636e\u4e2d\uff0cGM12878\u548cIMR90\u7ec6\u80de\u7cfb\u4e4b\u95f4\u7684\u5dee\u5f02\u53ef\u89c6\u5316\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>data(&#8220;GM12878.40kb.raw.chr2&#8221;)<\/p>\n<p>data(&#8220;IMR90.40kb.raw.chr2&#8221;)<\/p>\n<p>mtx1 &lt;- GM12878.40kb.raw.chr2<\/p>\n<p>mtx2 &lt;- IMR90.40kb.raw.chr2<\/p>\n<p>res &lt;- 40000 # Set resolution<\/p>\n<p>#\u5168\u5c40\u6807\u51c6\u5316\u77e9\u9635\uff0c\u4ee5\u4fbf\u4e8e\u8fdb\u884c\u66f4\u76f4\u89c2\u7684\u6bd4\u8f83\uff08\u4e0d\u4f1a\u5f71\u54cdTAD\u8c03\u7528\uff09<\/p>\n<p>mtx1_total &lt;- sum(mtx1)<\/p>\n<p>mtx2_total &lt;- sum(mtx2)<\/p>\n<p>(scaling_factor &lt;- mtx1_total \/ mtx2_total)<\/p>\n<p>## [1] 0.3837505<\/p>\n<p>#\u6839\u636e\u54ea\u4e2a\u77e9\u9635\u8f83\u5c0f\u6765\u91cd\u65b0\u8c03\u6574\u77e9\u9635\u7684\u5927\u5c0f\u3002<\/p>\n<p>if (mtx1_total &gt; mtx2_total) {<\/p>\n<p>mtx2 &lt;- mtx2 * scaling_factor<\/p>\n<p>} else {<\/p>\n<p>mtx1 &lt;- mtx1 * (1 \/ scaling_factor)<\/p>\n<p>}<\/p>\n<p>#\u6709\u8da3\u7684\u533a\u57df\u7684\u5750\u6807<\/p>\n<p>start_coord &lt;- 8000000<\/p>\n<p>end_coord &lt;- 16000000<\/p>\n<p>#\u53e6\u4e00\u4e2a\u6709\u8da3\u7684\u5750\u6807<\/p>\n<p># start_coord &lt;- 40000000<\/p>\n<p># end_coord &lt;- 48000000<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>4.5.1 \u6bd4\u8f83TAD\u8fb9\u754c\u5206\u6570<\/strong><\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u8fd0\u884cTADCompare\u7684\u5f53\u524d\u7248\u672c<\/p>\n<p>TD_Compare &lt;- TADCompare(mtx1, mtx2, resolution = res)<\/p>\n<p>#\u8fd0\u884c\u9884\u5148\u89c4\u5b9a\u7684TADs\u7ed8\u56fe\u7b97\u6cd5<\/p>\n<p>p &lt;- DiffPlot(tad_diff = TD_Compare,<\/p>\n<p>cont_mat1 = mtx1,<\/p>\n<p>cont_mat2 = mtx2,<\/p>\n<p>resolution = res,<\/p>\n<p>start_coord = start_coord,<\/p>\n<p>end_coord = end_coord,<\/p>\n<p>show_types = TRUE,<\/p>\n<p>point_size = 5,<\/p>\n<p>max_height = 5,<\/p>\n<p>rel_heights = c(1, 2),<\/p>\n<p>palette = &#8220;RdYlBu&#8221;)<\/p>\n<p>## Warning: The `&lt;scale&gt;` argument of `guides()` cannot be `FALSE`. Use &#8220;none&#8221; instead as<\/p>\n<p>## of ggplot2 3.3.4.<\/p>\n<p>## \u2139 The deprecated feature was likely used in the TADCompare package.<\/p>\n<p>## Please report the issue at<\/p>\n<p>## &lt;https:\/\/github.com\/dozmorovlab\/TADCompare\/issues&gt;.<\/p>\n<p>## This warning is displayed once every 8 hours.<\/p>\n<p>## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was<\/p>\n<p>## generated.<\/p>\n<p>plot(p)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"1270\" height=\"761\" class=\"wp-image-16133\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2.png\" srcset=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2.png 1270w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2-300x180.png 300w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2-1024x614.png 1024w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2-768x460.png 768w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-2-600x360.png 600w\" sizes=\"(max-width: 1270px) 100vw, 1270px\" \/><\/p>\n<p>\u4ece\u8fd9\u4e9b\u7ed3\u679c\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u4e24\u4e2a\u77e9\u9635\uff08\u201cBoundary score 1\u201d\u548c\u201cBoundary score 2\u201d\uff09\u4e2d\u7684\u8fb9\u754c\u5f97\u5206\u7ecf\u5e38\u88ab\u68c0\u6d4b\u4e3a\u663e\u8457\u8fb9\u754c\uff08\u8fb9\u754c\u5f97\u5206\u9ad8\u4e8e1.5\u7684\u9608\u503c\uff09\uff0c\u4f46\u5b83\u4eec\u662f\u975e\u5dee\u5f02\u6027\u7684\uff08\u9ed1\u8272\u5706\u70b9\uff09\u3002\u5dee\u5f02\u6027\u8fb9\u754c\u5bf9\u5e94\u4e8e\u201cDifferential boundary score\u201d\u8f68\u8ff9\uff0c\u5176\u4e2d\u68c0\u6d4b\u5230\u7edd\u5bf9\u8fb9\u754c\u5f97\u5206\u5dee\u5f02\u9ad8\u4e8e2.0\u7684\u9608\u503c\u3002\u4e0d\u540c\u7c7b\u578b\u7684\u5dee\u5f02\u6027\u8fb9\u754c\u6839\u636eTADCompare\u624b\u7a3f\u4e2d\u63cf\u8ff0\u7684\u6a21\u5f0f\u8fdb\u884c\u5b9a\u4e49\u3002\u8bf7\u6ce8\u610f\uff0c\u901a\u8fc7\u5c06\u201cshow_types\u201d\u8bbe\u7f6e\u4e3aFALSE\uff0c\u53ef\u4ee5\u7981\u7528\u6309\u7c7b\u578b\u7740\u8272\uff1b\u53ea\u4f1a\u663e\u793a\u5dee\u5f02\u6027\u548c\u975e\u5dee\u5f02\u6027\u6807\u7b7e\u3002<\/p>\n<p><strong>4.5.2 \u6bd4\u8f83\u9884\u5b9a\u4e49\u7684TAD\u8fb9\u754c<\/strong><\/p>\n<p>\u6211\u4eec\u8fd8\u53ef\u4ee5\u63d0\u4f9b\u5305\u542b\u6bcf\u4e2a\u63a5\u89e6\u77e9\u9635\u7684TAD\u8fb9\u754c\u7684TAD\u5750\u6807\u5217\u8868\u6765\u4f7f\u7528\u9884\u6307\u5b9a\u7684TAD\u3002\u8be5\u5217\u8868\u7684\u957f\u5ea6\u5e94\u4e3a2\u3002\u4e0b\u9762\u6211\u4eec\u5c06\u5c55\u793a\u5982\u4f55\u4f7f\u7528SpectralTAD\u8fdb\u884c\u9884\u6307\u5b9a\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u8c03\u7528SpectralTAD\u8fdb\u884c\u62d3\u6251\u5173\u8054\u57df\u5206\u6790<\/p>\n<p>bed_coords1 = bind_rows(SpectralTAD(mtx1, chr = &#8220;chr2&#8221;, levels = 3))<\/p>\n<p>## Estimating resolution<\/p>\n<p>bed_coords2 = bind_rows(SpectralTAD::SpectralTAD(mtx2, chr = &#8220;chr2&#8221;, levels = 3))<\/p>\n<p>## Estimating resolution<\/p>\n<p>#\u5c06\u6570\u636e\u653e\u5165\u5217\u8868\u4ee5\u8fdb\u884c\u7ed8\u56fe\u8fc7\u7a0b<\/p>\n<p>Combined_Bed = list(bed_coords1, bed_coords2)<\/p>\n<p>#\u8fd0\u884c\u5e26\u6709\u9884\u5148\u89c4\u5b9a\u7684 TADs \u7684 TADCompare<\/p>\n<p>TD_Compare &lt;- TADCompare(mtx1, mtx2, resolution = res, pre_tads = Combined_Bed)<\/p>\n<p>#\u8fd0\u884c\u9884\u5148\u89c4\u5b9a\u7684TADs\u7ed8\u56fe\u7b97\u6cd5<\/p>\n<p>p &lt;- DiffPlot(tad_diff = TD_Compare,<\/p>\n<p>cont_mat1 = mtx1,<\/p>\n<p>cont_mat2 = mtx2,<\/p>\n<p>resolution = res,<\/p>\n<p>start_coord = start_coord,<\/p>\n<p>end_coord = end_coord,<\/p>\n<p>pre_tad = Combined_Bed,<\/p>\n<p>show_types = FALSE,<\/p>\n<p>point_size = 5,<\/p>\n<p>max_height = 10,<\/p>\n<p>rel_heights = c(1.5, 2),<\/p>\n<p>palette = &#8220;RdYlBu&#8221;)<\/p>\n<p>plot(p)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"1267\" height=\"762\" class=\"wp-image-16134\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file.png\" alt=\"\u56fe\u793a\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file.png 1267w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file-300x180.png 300w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file-1024x616.png 1024w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file-768x462.png 768w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/unnamed-file-600x361.png 600w\" sizes=\"(max-width: 1267px) 100vw, 1267px\" \/><\/p>\n<p>\u6b63\u5982\u6211\u4eec\u6240\u770b\u5230\u7684\uff0c\u9884\u5148\u89c4\u5b9a\u7684TADs\u5141\u8bb8\u6211\u4eec\u52fe\u52d2\u51faTAD\u8fb9\u754c\uff0c\u4ece\u800c\u589e\u5f3a\u53ef\u89c6\u5316\u6548\u679c\u3002\u6b64\u5916\uff0c\u73b0\u5728\u5448\u73b0\u7684\u5dee\u5f02\u8fb9\u754c\u4e0e\u90a3\u4e9b\u7531TAD\u8c03\u7528\u8005\u8c03\u7528\u7684\u8fb9\u754c\u76f8\u5bf9\u5e94\uff0c\u800c\u4e0d\u662f\u90a3\u4e9b\u7531TADCompare\u4f7f\u7528\u8fb9\u754c\u5206\u6570\u68c0\u6d4b\u5230\u7684\u8fb9\u754c\u3002\u8bf7\u6ce8\u610f\uff0c\u9884\u5148\u89c4\u5b9a\u7684TAD\u8fb9\u754c\u5e76\u4e0d\u4e00\u5b9a\u5bf9\u5e94\u4e8e\u8fb9\u754c\u5206\u6570\uff1b\u56e0\u6b64\uff0c\u5206\u7c7b\u6a21\u5f0f\u662f\u6839\u636e\u9884\u5b9a\u4e49\u7684TAD\u8fb9\u754c\u5e94\u7528\u7684\u3002\u7136\u800c\uff0c\u4f7f\u7528\u9884\u5148\u89c4\u5b9a\u7684TADs\u4f7f\u5f97\u89c6\u89c9\u4e0a\u66f4\u5bb9\u6613\u89e3\u91ca\u5dee\u5f02\u7684\u5dee\u5f02\u3002\u56e0\u6b64\uff0c\u6211\u4eec\u5efa\u8bae\u5c06\u201cshow_types\u201d\u8bbe\u7f6e\u4e3aFALSE\u3002\u6b64\u5916\uff0c\u5bf9\u4e8e\u9884\u5148\u89c4\u5b9a\u7684TADs\uff0c\u5f15\u5165\u4e86\u4e00\u4e2a\u540d\u4e3a\u201cNon-Overlap\u201d\u7684\u65b0\u7c7b\u522b\u3002\u975e\u91cd\u53e0\u5bf9\u5e94\u4e8e\u88abTADCompare\u786e\u5b9a\u4e3a\u975e\u5dee\u5f02\u7684\u8fb9\u754c\uff0c\u4f46\u5728\u88abTAD\u8c03\u7528\u8005\u8c03\u7528\u65f6\u4e0d\u91cd\u53e0\u3002<\/p>\n<p><strong>5 TimeCompare<\/strong><\/p>\n<p><strong>5.1 \u4ecb\u7ecd<\/strong><\/p>\n<p>TimeCompare\u662f\u4e00\u4e2a\u7528\u4e8e\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u5206\u6790\u7684\u51fd\u6570\u3002\u7b80\u5355\u6765\u8bf4\uff0c\u7528\u6237\u8f93\u5165\u4e00\u4e2a\u4ee3\u8868\u81f3\u5c11\u56db\u4e2a\u65f6\u95f4\u70b9\u7684\u63a5\u89e6\u77e9\u9635\u5217\u8868\u3002TimeCompare\u51fd\u6570\u53ef\u4ee5\u5904\u7406\u8f83\u5c11\u7684\u65f6\u95f4\u70b9\uff0c\u4f46\u65f6\u95f4\u53d8\u5316\u7684\u5206\u7c7b\u53ef\u80fd\u4f1a\u51fa\u9519\u3002\u8f93\u51fa\u662f\u4e00\u4e2a\u5305\u542b\u5728\u81f3\u5c11\u4e00\u4e2a\u65f6\u95f4\u70b9\u68c0\u6d4b\u5230\u7684\u6240\u6709\u5177\u6709TAD\u8fb9\u754c\u7684\u533a\u57df\u7684\u6570\u636e\u6846\u3002\u8fd9\u4e9b\u533a\u57df\u6839\u636eTAD\u8fb9\u754c\u968f\u65f6\u95f4\u5982\u4f55\u6f14\u53d8\u8fdb\u4e00\u6b65\u5206\u4e3a\u516d\u79cd\u4e0d\u540c\u7684\u65f6\u95f4\u53d8\u5316\u7c7b\u578b\uff08\u9ad8\u5ea6\u5e38\u89c1\u3001\u52a8\u6001\u3001\u65e9\u671f\/\u665a\u671f\u51fa\u73b0\u548c\u65e9\u671f\/\u665a\u671f\u6d88\u5931\uff09\u3002\u8be5\u51fd\u6570\u8fd8\u8fd4\u56de\u4e00\u4e2a\u603b\u7ed3\u6bcf\u4e2aTAD\u8fb9\u754c\u51fa\u73b0\u7684\u56fe\uff0c\u4ee5\u53ca\u53e6\u4e00\u4e2a\u5305\u542b\u6bcf\u4e2a\u533a\u57df\u7684\u66f4\u6539\u6458\u8981\u7684\u6570\u636e\u6846\uff0c\u65e0\u8bba\u662f\u5426\u68c0\u6d4b\u5230\u8fb9\u754c\u3002<\/p>\n<p><strong>5.2 \u8fd0\u884c<\/strong><\/p>\n<p>TimeCompare\u51fd\u6570\u63a5\u6536\u4e00\u7ec4\u683c\u5f0f\u7c7b\u4f3c\u4e8eTADCompare\u51fd\u6570\u7684\u77e9\u9635\u3002\u4e0eTADCompare\u4e00\u6837\uff0cTimeCompare\u51fd\u6570\u5c06\u4f30\u8ba1\u5206\u8fa8\u7387\u5e76\u5c06\u77e9\u9635\u8f6c\u6362\u4e3a\u9002\u5f53\u7684\u683c\u5f0f\u3002\u5728\u8fd9\u4e2a\u4f8b\u5b50\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528\u65f6\u95f4\u53d8\u5316\u4e0b\u7684\u7a00\u758f3\u5217\u63a5\u89e6\u77e9\u9635\uff0c\u8868\u793aHCT-116\u7ec6\u80de\u7cfb\u3002\u8fd9\u4e9b\u77e9\u9635\u4ee3\u8868\u7528TAD\u8fb9\u754c\u7834\u574f\u7684\u690d\u7269\u751f\u957f\u7d20\u5904\u7406\u7684\u4e00\u4e2a\u5355\u72ec\u7684\u67d3\u8272\u4f5322\u7ec6\u80de\u6837\u672c\u3002\u6570\u636e\u7136\u540e\u5728\u690d\u7269\u751f\u957f\u7d20\u64a4\u51fa\u540e\u56db\u4e2a\u65f6\u95f4\u70b9\uff0820\u300140\u300160\u548c180\u5206\u949f\uff09\u8fdb\u884c\u6d4b\u5e8f\u3002\u4e00\u65e6\u690d\u7269\u751f\u957f\u7d20\u88ab\u64a4\u51fa\uff0cTAD\u8fb9\u754c\u4f1a\u6162\u6162\u6062\u590d\u3002\u4f7f\u7528TimeCompare\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u8ffd\u8e2a\u690d\u7269\u751f\u957f\u7d20\u64a4\u51fa\u540e\u7684TADs\u7684\u6062\u590d\u60c5\u51b5\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u83b7\u53d6\u8054\u7cfb\u77e9\u9635\u7684\u5217\u8868<\/p>\n<p>data(&#8220;time_mats&#8221;)<\/p>\n<p>#\u68c0\u67e5\u683c\u5f0f<\/p>\n<p>head(time_mats[[1]])<\/p>\n<p>## # A tibble: 6 \u00d7 3<\/p>\n<p>## X1 X2 X3<\/p>\n<p>## &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;<\/p>\n<p>## 1 16050000 16050000 14<\/p>\n<p>## 2 16100000 16100000 3<\/p>\n<p>## 3 16200000 16200000 1<\/p>\n<p>## 4 16250000 16250000 1<\/p>\n<p>## 5 16300000 16300000 10<\/p>\n<p>## 6 16350000 16350000 2<\/p>\n<p>#\u8fd9\u4e9b\u662f\u7a00\u758f\u7684\u4e09\u5217\u77e9\u9635<\/p>\n<p>#\u8fd0\u884cTimeCompare<\/p>\n<p>time_var &lt;- TimeCompare(time_mats, resolution = 50000)<\/p>\n<p>## Converting to n x n matrix<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>TimeCompare\u51fd\u6570\u8fd4\u56de\u7684\u7b2c\u4e00\u4e2a\u9879\u76ee\u662fTAD_Bounds\uff0c\u8fd9\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u5305\u542b\u4e86\u5728\u81f3\u5c11\u4e00\u4e2a\u65f6\u95f4\u70b9\u68c0\u6d4b\u5230\u7684TAD\u8fb9\u754c\u7684\u6240\u6709\u533a\u57df\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>head(time_var$TAD_Bounds)<\/p>\n<p>## Coordinate Sample 1 Sample 2 Sample 3 Sample 4 Consensus_Score<\/p>\n<p>## 1 16900000 -0.6733709 -0.7751516 -0.7653696 15.1272252 -0.71937026<\/p>\n<p>## 2 17350000 3.6406563 2.3436229 3.0253018 0.7840556 2.68446232<\/p>\n<p>## 3 18850000 0.6372268 6.3662244 -0.7876844 6.9255446 3.50172562<\/p>\n<p>## 4 20700000 1.5667926 3.0968633 2.9130479 2.8300136 2.87153075<\/p>\n<p>## 5 22000000 -1.0079676 -0.7982571 0.6007264 3.1909178 -0.09876534<\/p>\n<p>## 6 22050000 -1.0405532 -0.9892242 -0.2675822 4.2737511 -0.62840320<\/p>\n<p>## Category<\/p>\n<p>## 1 Late Appearing TAD<\/p>\n<p>## 2 Early Disappearing TAD<\/p>\n<p>## 3 Early Appearing TAD<\/p>\n<p>## 4 Dynamic TAD<\/p>\n<p>## 5 Late Appearing TAD<\/p>\n<p>## 6 Late Appearing TAD<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u7b2c\u4e00\u5217\u5bf9\u5e94\u4e8e\u57fa\u56e0\u7ec4\u5750\u6807\u3002\u4ee5\u201cSample\u201d\u4e3a\u524d\u7f00\u7684\u5217\u5bf9\u5e94\u4e8e\u6bcf\u4e2a\u6837\u672c\u4e2d\u7ed9\u5b9a\u5750\u6807\u5904\u7684\u8fb9\u754c\u5f97\u5206\u3002\u5171\u8bc6\u5f97\u5206\u662f\u6240\u6709\u6837\u672c\u4e2d\u5f97\u5206\u7684\u4e2d\u4f4d\u6570\uff0c\u7c7b\u522b\u5bf9\u5e94\u4e8e\u53d8\u5316\u7684\u7c7b\u578b\u3002<\/p>\n<p>All_Bounds\u662f\u7b2c\u4e8c\u4e2a\u5217\u8868\u6761\u76ee\uff0c\u5176\u7ed3\u6784\u4e0eTAD_Bounds\u6570\u636e\u6846\u76f8\u540c\uff0c\u4f46\u5b83\u5305\u62ec\u4e86\u57fa\u56e0\u7ec4\u4e2d\u7684\u6bcf\u4e2a\u533a\u57df\uff0c\u65e0\u8bba\u5b83\u662f\u5426\u662f\u8f6c\u5f55\u8c03\u63a7\u533a\u57df\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td><a id=\"post-16131-_Hlk148655504\"><\/a> head(time_var$All_Bounds)<\/p>\n<p>## Coordinate Sample 1 Sample 2 Sample 3 Sample 4 Consensus_Score<\/p>\n<p>## 1 16900000 -0.6733709 -0.7751516 -0.7653696 15.1272252 -0.7193703<\/p>\n<p>## 2 16950000 -0.6343671 -0.6624276 -0.4107173 -0.6656620 -0.6483973<\/p>\n<p>## 3 17000000 -1.0409280 -0.7618272 0.7910678 -1.0008876 -0.8813574<\/p>\n<p>## 4 17050000 -0.9199917 -0.7123180 0.6712399 -0.8254422 -0.7688801<\/p>\n<p>## 5 17100000 -0.6097913 -0.4785485 -0.6232367 -0.2095729 -0.5441699<\/p>\n<p>## 6 17150000 -0.7215028 -0.5669957 0.2413230 -0.6332710 -0.6001333<\/p>\n<p>## Category<\/p>\n<p>## 1 Late Appearing TAD<\/p>\n<p>## 2 Highly Common TAD<\/p>\n<p>## 3 Highly Common TAD<\/p>\n<p>## 4 Highly Common TAD<\/p>\n<p>## 5 Highly Common TAD<\/p>\n<p>## 6 Highly Common TAD<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u8fd8\u6709\u4e00\u4e2a\u5806\u53e0\u6761\u5f62\u56fe\uff0c\u8be5\u56fe\u663e\u793a\u4e86\u6570\u636e\u4e2d\u6bcf\u79cd\u7c7b\u578b\u7684\u65f6\u95f4\u8fb9\u754c\u51fa\u73b0\u7684\u6b21\u6570\u3002\u8fd9\u4e2a\u56fe\u662f\u5728ggplot2\u4e2d\u521b\u5efa\u7684\uff0c\u5e76\u4e14\u662f\u5b8c\u5168\u53ef\u5b9a\u5236\u7684\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>time_var$Count_Plot<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"987\" height=\"654\" class=\"wp-image-16135\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-4.png\" srcset=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-4.png 987w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-4-300x199.png 300w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-4-768x509.png 768w, http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16131-4-600x398.png 600w\" sizes=\"(max-width: 987px) 100vw, 987px\" \/><\/p>\n<p><strong>6 ConsensusTAD<\/strong><\/p>\n<p><strong>6.1 \u4ecb\u7ecd<\/strong><\/p>\n<p>ConsensusTADs\u51fd\u6570\u5b9e\u73b0\u4e86\u4e00\u79cd\u5728\u591a\u4e2a\u6570\u636e\u96c6\u4e0a\u8c03\u7528TADs\u7684\u65b9\u6cd5\u3002\u5b83\u4f7f\u7528n\u4e2a\u91cd\u590d\u6216\u7ec6\u80de\u7cfb\u7684\u4e2d\u4f4d\u6570\u8fb9\u754c\u5f97\u5206\u6765\u8ba1\u7b97\u4e00\u81f4\u7684TAD\u8fb9\u754c\u5171\u8bc6\uff0c\u5373\u5728\u6240\u6709\u91cd\u590d\u4e2d\u4e00\u81f4\u68c0\u6d4b\u5230\u7684\u3002\u8fd9\u6709\u6548\u5730\u8fc7\u6ee4\u6389\u4e86\u53ea\u5728\u4e00\u4e24\u4e2a\u91cd\u590d\u6216\u7ec6\u80de\u7cfb\u4e2d\u51fa\u73b0\u7684\u566a\u58f0TAD\u8fb9\u754c\u3002<\/p>\n<p><strong>6.2 \u8fd0\u884c<\/strong><\/p>\n<p>ConsensusTADs\u51fd\u6570\u4e0eTimeCompare\u51fd\u6570\u5177\u6709\u57fa\u672c\u76f8\u540c\u7684\u8f93\u5165\uff08\u4e00\u4e2a\u63a5\u89e6\u77e9\u9635\u5217\u8868\uff09\u3002\u5b83\u4e3a\u6bcf\u4e2a\u533a\u57df\u63d0\u4f9b\u5171\u8bc6TAD\u5206\u6570\uff0c\u5e76\u5728\u57fa\u56e0\u7ec4\u7684\u6bcf\u4e2a\u63a5\u89e6\u77e9\u9635\u4e0a\u8fdb\u884c\u6c47\u603b\u3002\u5b83\u8fd8\u63d0\u4f9b\u4e86\u4e00\u7ec4\u5177\u6709\u663e\u8457TAD\u5206\u6570\u7684\u533a\u57df\u3002\u8fd9\u4e9b\u533a\u57df\u53ef\u4ee5\u88ab\u89c6\u4e3a\u5171\u8bc6TAD\u8fb9\u754c\u3002\u901a\u8fc7\u4f7f\u7528\u8fd9\u4e9b\u8fb9\u754c\uff0c\u6211\u4eec\u53ef\u4ee5\u5728\u4e00\u7ec4\u91cd\u590d\u3001\u6761\u4ef6\u6216\u65f6\u95f4\u70b9\u4e0a\u83b7\u5f97\u4e00\u7ec4\u5355\u4e00\u7684TAD\u6c47\u603b\u3002\u5728\u672c\u4f8b\u4e2d\uff0c\u6211\u4eec\u4f7f\u7528\u4e24\u4e2a\u91cd\u590d\u6837\u672c\u3002<\/p>\n<p>\u6211\u4eec\u6f14\u793a\u4e86\u5982\u4f55\u901a\u8fc7\u8c03\u7528\u5171\u8bc6TADs\u6765\u8fd0\u884cConsensusTADs\uff0c\u8be5\u51fd\u6570\u5bf9\u5355\u4e2a\u4f53\u6837\u54c1\u8fdb\u884c\u5904\u7406\u540e\u521b\u5efa\u7684\u65f6\u95f4\u53d8\u5316\u63a5\u89e6\u77e9\u9635\u8fdb\u884c\u64cd\u4f5c\uff0c\u5176\u4e2d\u5904\u7406\u7834\u574f\u4e86\u5176TAD\u8fb9\u754c\uff0c\u7136\u540e\u8ddf\u8e2a\u5b83\u4eec\u5728\u56db\u4e2a\u65f6\u95f4\u70b9\uff0820\u300140\u300160\u548c180\u5206\u949f\uff09\u7684\u8fd4\u56de\u3002\u5171\u8bc6\u8fb9\u754c\u5f97\u5206\u65e8\u5728\u63d0\u4f9b\u6240\u6709\u65f6\u95f4\u70b9\u7684TAD\u8fb9\u754c\u7684\u603b\u7ed3\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>#\u83b7\u53d6\u5305\u5185\u6784\u5efa\u7684RAO\u63a5\u89e6\u77e9\u9635\u3002<\/p>\n<p>data(&#8220;time_mats&#8221;)<\/p>\n<p>#\u8fd0\u884cConsensusTADs<\/p>\n<p>con_tads &lt;- ConsensusTADs(time_mats, resolution = 50000)<\/p>\n<p>## Converting to n x n matrix<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/p>\n<p>## Matrix dimensions: 704&#215;704<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>ConsensusTADs \u51fd\u6570\u8fd4\u56de\u4e24\u4e2a\u6570\u636e\u6846\u3002\u7b2c\u4e00\u4e2a\u6570\u636e\u6846\uff0cConsensus\uff0c\u5305\u542b\u4e86\u57fa\u4e8e\u5171\u8bc6\u5f97\u5206\u7684\u6240\u6709\u5305\u542b\u5171\u8bc6 TADs \u7684\u533a\u57df\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>head(con_tads$Consensus)<\/p>\n<p>## Coordinate Sample 1 Sample 2 Sample 3 Sample 4 Consensus_Score<\/p>\n<p>## 1 16900000 -0.6733709 -0.7751516 -0.7653696 15.1272252 -0.71937026<\/p>\n<p>## 2 17350000 3.6406563 2.3436229 3.0253018 0.7840556 2.68446232<\/p>\n<p>## 3 18850000 0.6372268 6.3662244 -0.7876844 6.9255446 3.50172562<\/p>\n<p>## 4 20700000 1.5667926 3.0968633 2.9130479 2.8300136 2.87153075<\/p>\n<p>## 5 22000000 -1.0079676 -0.7982571 0.6007264 3.1909178 -0.09876534<\/p>\n<p>## 6 22050000 -1.0405532 -0.9892242 -0.2675822 4.2737511 -0.62840320<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u5217\u5bf9\u5e94\u4e8e\u5177\u6709\u663e\u8457\u8fb9\u754c\u5f97\u5206\u7684\u533a\u57df\u7684\u5750\u6807\uff0c\u6bcf\u4e2a\u533a\u57df\u7684\u4e2a\u4f53\u8fb9\u754c\u5f97\u5206\u4ee5\u53ca\u5171\u8bc6\u5f97\u5206\u3002<\/p>\n<p>\u7b2c\u4e8c\u4e2a\u6570\u636e\u6846All_Regions\u4e0eConsensus\u6570\u636e\u6846\u76f8\u540c\uff0c\u4f46\u5b83\u5305\u62ec\u57fa\u56e0\u7ec4\u4e2d\u51fa\u73b0\u5728\u4e24\u4e2a\u77e9\u9635\u4e2d\u7684\u6bcf\u4e2a\u533a\u57df\u3002<\/p>\n<table>\n<tbody>\n<tr>\n<td>head(con_tads$All_Regions)<\/p>\n<p>## Coordinate Sample 1 Sample 2 Sample 3 Sample 4 Consensus_Score<\/p>\n<p>## 1 16900000 -0.6733709 -0.7751516 -0.7653696 15.1272252 -0.7193703<\/p>\n<p>## 2 16950000 -0.6343671 -0.6624276 -0.4107173 -0.6656620 -0.6483973<\/p>\n<p>## 3 17000000 -1.0409280 -0.7618272 0.7910678 -1.0008876 -0.8813574<\/p>\n<p>## 4 17050000 -0.9199917 -0.7123180 0.6712399 -0.8254422 -0.7688801<\/p>\n<p>## 5 17100000 -0.6097913 -0.4785485 -0.6232367 -0.2095729 -0.5441699<\/p>\n<p>## 6 17150000 -0.7215028 -0.5669957 0.2413230 -0.6332710 -0.6001333<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><strong>7 \u7ed3\u8bed<\/strong><\/p>\n<p>\u770b\u4e86\u8fd9\u4e48\u591a\uff0c\u5c0f\u4f19\u4f34\u53ef\u80fd\u6709\u4e9b\u6655\u4e4e\u4e4e\u7684\uff0c\u5927\u6d77\u54e5\u6765\u603b\u7ed3\u4e00\u4e0b\u3002TADCompare\u6709\u4e09\u4e2a\u4e3b\u8981\u529f\u80fd\uff1aTADCompare\u7528\u4e8e\u5dee\u5f02\u6027TAD\u5206\u6790\uff0cTimeCompare\u7528\u4e8e\u65f6\u95f4\u5e8f\u5217\u5206\u6790\uff0cConsensusTADs\u7528\u4e8e\u5171\u8bc6\u8fb9\u754c\u8bc6\u522b\u3002<\/p>\n<p>TimeCompare\u662f\u4e00\u4e2a\u529f\u80fd\u5f3a\u5927\u3001\u64cd\u4f5c\u7b80\u4fbf\u7684\u65f6\u95f4\u5e8f\u5217\u6570\u636e\u5206\u6790\u5de5\u5177\u3002\u5927\u6d77\u54e5\u76f8\u4fe1\u65e0\u8bba\u662f\u5bf9\u4e8e\u5b66\u672f\u7814\u7a76\u8fd8\u662f\u5b9e\u9645\u5e94\u7528\uff0c\u90fd\u6709\u5f88\u5927\u7684\u5e2e\u52a9\u3002<\/p>\n<p>\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1a(http:\/\/www.biocloudservice.com\/home.html)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/313\/313.php)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/906\/906.php)\u7b49\u5404\u79cd\u5c0f\u5de5\u5177\u54e6\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u767b\u5f55\u7f51\u7ad9\u8fdb\u884c\u4e86\u89e3 (http:\/\/www.biocloudservice.com\/home.html) \u3002<\/p>\n<p><strong>\u53c2\u8003\u6587\u732e<\/strong><\/p>\n<p>Cresswell, K. G., &amp; Dozmorov, M. G. (2020). TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains. Frontiers in genetics, 11, 158. https:\/\/doi.org\/10.3389\/fgene.2020.00158<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u5c0f\u4f19\u4f34\u4eec\u597d\u554a\uff01\u4e0d\u77e5\u9053\u5927\u5bb6\u6709\u6ca1\u6709\u5206\u6790\u62d3\u6251\u76f8\u5173\u57df\uff08Topologically Associated Domains [&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\/16131"}],"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=16131"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/16131\/revisions"}],"predecessor-version":[{"id":16136,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/16131\/revisions\/16136"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16131"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16131"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16131"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}