{"id":61763,"date":"2024-11-19T15:18:30","date_gmt":"2024-11-19T07:18:30","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61763"},"modified":"2024-11-19T15:18:30","modified_gmt":"2024-11-19T07:18:30","slug":"%e9%98%b5%e5%88%97cgh%e6%95%b0%e6%8d%ae%e6%97%a0%e4%bb%8e%e4%b8%8b%e6%89%8b%ef%bc%9fglad%e5%8c%85%e5%b8%a6%e4%bd%a0%e7%a9%bf%e8%b6%8a%e5%9f%ba%e5%9b%a0%e7%bb%84%e7%9a%84%e6%96%ad%e7%82%b9%e8%bf%b7","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61763","title":{"rendered":"\u9635\u5217CGH\u6570\u636e\u65e0\u4ece\u4e0b\u624b\uff1fGLAD\u5305\u5e26\u4f60\u7a7f\u8d8a\u57fa\u56e0\u7ec4\u7684\u65ad\u70b9\u8ff7\u5bab\uff01"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>\u563f\u670b\u53cb\u4eec\uff0c\u5c0f\u679c\u5411\u5bfc\u53c8\u6765\u5566\uff0c\u6b22\u8fce\u6765\u5230\u751f\u7269\u4fe1\u606f\u5b66\u7684\u5947\u5999\u4e16\u754c\u3002\u4eca\u5929\uff0c\u6211\u4eec\u8981\u4e00\u8d77\u8e0f\u4e0a\u4e00\u573a<a>\u9635\u5217CGH<\/a>\uff08\u6bd4\u8f83\u57fa\u56e0\u7ec4\u6742\u4ea4\uff09\u6570\u636e\u7684\u63a2\u7d22\u4e4b\u65c5<a>\u3002<\/a><\/p>\n\n\n\n<p><a><\/a>\u9635\u5217CGH\uff0c\u542c\u8d77\u6765\u662f\u4e0d\u662f\u6709\u70b9\u795e\u79d8\uff1f\u5176\u5b9e\uff0c\u8fd9\u5c31\u662f\u6211\u4eec\u7684\u8d85\u7ea7\u4fa6\u63a2\u5de5\u5177\uff0c\u80fd\u5728\u57fa\u56e0\u7ec4\u7684\u6d77\u6d0b\u4e2d\u5bfb\u627eDNA\u7684\u589e\u52a0\u6216\u7f3a\u5931\u3002\u8fd9\u4e9b\u5fae\u5c0f\u7684\u53d8\u5316\u53ef\u80fd\u662f\u75be\u75c5\u7684\u7f6a\u9b41\u7978\u9996\uff0c\u6bd4\u5982\u8ba9\u4eba\u95fb\u98ce\u4e27\u80c6\u7684\u764c\u75c7\uff0c\u6216\u662f\u795e\u79d8\u7684\u795e\u7ecf\u53d1\u80b2\u969c\u788d\u7b49\u7b49\u3002\u9635\u5217CGH\u5c31\u50cf\u4e00\u5f20\u5b9d\u56fe\uff0c\u4e0a\u9762\u7684\u4e00\u7cfb\u5217\u5bf9\u6570\u6bd4\u503c\u5c31\u662f\u7ebf\u7d22\uff0c\u6307\u5f15\u6211\u4eec\u53d1\u73b0\u6d4b\u8bd5\u6837\u672c\u548c\u53c2\u8003\u6837\u672c\u5728\u57fa\u56e0\u7ec4\u5404\u533a\u57df\u7684DNA\u62f7\u8d1d\u6570\u7684\u5dee\u5f02\u3002\u8fd9\u5c31\u50cf\u662f\u4e00\u573a\u5bfb\u5b9d\u6e38\u620f\uff0c\u4f60\u51c6\u5907\u597d\u52a0\u5165\u6211\u4eec\uff0c\u4e00\u8d77\u63ed\u5f00\u57fa\u56e0\u7ec4\u7684\u795e\u79d8\u9762\u7eb1\u4e86\u5417\uff1f<\/p>\n\n\n\n<p>\u5728\u8fd9\u4e2a\u65c5\u7a0b\u4e2d\uff0c\u6211\u4eec\u7684\u5f97\u529b\u52a9\u624b\u662fGLAD\u5305\u3002\u6211\u4eec\u5c06\u7528\u5b83\u6765\u5bfb\u627e\u90a3\u4e9b\u9690\u85cf\u5728\u57fa\u56e0\u7ec4\u6df1\u5904\u7684\u65ad\u70b9\uff0c\u5e76\u4e3a\u6bcf\u4e2a\u795e\u79d8\u7684\u67d3\u8272\u4f53\u533a\u57df\u5206\u914d\u4e00\u4e2a\u8eab\u4efd\u6807\u7b7e\u2014\u2014\u6b63\u5e38\u3001\u589e\u52a0\u6216\u7f3a\u5931\u3002<strong>\u6ce8\u610f\u54e6\uff0cGLAD<\/strong><strong>\u5305\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668<\/strong><strong>\u54e6<\/strong><strong>\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\u6027\u4ef7\u6bd4\u9ad8\u7684\u670d\u52a1\u5668<\/strong><strong>~<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u4e0b\u9762\uff0c\u5c0f\u679c\u5c06\u5f15\u9886\u5927\u5bb6\u9010\u6b65\u638c\u63e1\u64cd\u4f5c\u6d41\u7a0b\uff0c\u4ece\u6570\u636e\u9884\u5904\u7406\u5f00\u59cb\uff0c\u5230\u5bfb\u627e\u57fa\u56e0\u7ec4\u65ad\u70b9\uff0c\u518d\u5230\u786e\u5b9a\u67d3\u8272\u4f53\u533a\u57df\u7684\u72b6\u6001\uff0c\u6211\u4eec\u5c06\u4e00\u540c\u63ed\u793a\u9635\u5217CGH\u6570\u636e\u5206\u6790\u7684\u5965\u79d8\u3002<strong>\u5982\u679c\u4f60\u5728\u65c5\u9014\u4e2d\u9047\u5230\u4efb\u4f55\u56f0\u96be\uff0c\u522b\u62c5\u5fc3\uff0c<\/strong><strong>\u5c0f\u679c<\/strong><strong>\u968f\u65f6\u5f85\u547d\uff0c<\/strong><strong>\u8bb0\u5f97\u8054\u7cfb\u5c0f\u679c<\/strong><strong>\u4e3a\u4f60\u89e3\u7b54\u7591\u60d1<\/strong><strong>~<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u5148\u5b89\u88c5\u5e76\u52a0\u8f7dGLAD\u5305\uff1a<\/p>\n\n\n\n<p>if (!require(&#8220;BiocManager&#8221;, quietly = TRUE))<\/p>\n\n\n\n<p>&nbsp;&nbsp;install.packages(&#8220;BiocManager&#8221;)<\/p>\n\n\n\n<p>BiocManager::install(&#8220;GLAD&#8221;)<\/p>\n\n\n\n<p>require(GLAD)<\/p>\n\n\n\n<p>\u5728GLAD\u5305\u4e2d\uff0c\u9635\u5217 CGH \u8c31\u5206\u6790\u6709\u4e24\u4e2a\u51fd\u6570\u53ef\u7528\uff1aglad \u548c daglad\u3002\u7b2c\u4e8c\u4e2a\u51fd\u6570\u662f\u7b2c\u4e00\u4e2a\u51fd\u6570\u7684\u6539\u8fdb\uff0c\u56e0\u6b64\u66f4\u5efa\u8bae\u4f7f\u7528 daglad \u51fd\u6570\u3002\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5c06\u4e3a\u4f60\u6f14\u793a\u8fd9\u4e24\u4e2a\u51fd\u6570\u7684\u4f7f\u7528\u65b9\u6cd5\u3002\u8bf7\u6ce8\u610f\uff0c\u4f7f\u7528\u9009\u9879 smoothfunc=haarseg\u53ef\u4ee5\u52a0\u5feb\u8ba1\u7b97\u901f\u5ea6\u54e6~<\/p>\n\n\n\n<ul>\n<li>glad\u51fd\u6570<\/li>\n<\/ul>\n\n\n\n<p>\u7b2c\u4e00\u6b65\uff0c\u83b7\u53d6\u6570\u636e\u3002\u6211\u4eec\u4f7f\u7528\u6765\u81ea Snijders \u7b49\u4eba (2001) \u7684\u516c\u5171\u6570\u636e\u96c6\u3002\u6570\u636e\u5bf9\u5e94\u4e8e NIGMS \u4eba\u7c7b\u9057\u4f20\u5b66\u7ec6\u80de\u5e93 (http:\/\/locus.umdnj.edu\/nigms) \u4e2d 15 \u79cd\u5df2\u77e5\u6838\u578b\u7684\u4eba\u7c7b\u7ec6\u80de\u682a \uff0812 \u79cd\u6210\u7ea4\u7ef4\u7ec6\u80de\u682a\u30012 \u79cd\u7ed2\u6bdb\u7ec6\u80de\u682a\u30011 \u79cd\u6dcb\u5df4\u6bcd\u7ec6\u80de\u682a\uff09\u3002 \u6bcf\u79cd\u7ec6\u80de\u682a\u5747\u5728 2276 \u4e2a BAC \u7684 CGH \u9635\u5217\u4e0a\u8fdb\u884c\u6742\u4ea4\uff0c\u5e76\u91cd\u590d\u4e09\u6b21\u3002\u52a0\u8f7d\u6570\u636e\u540e\uff0c\u9700\u8981\u5c06gm13330\u7ec6\u80de\u7cfb\u7684\u6570\u636e<a>\u521b\u5efa\u4e3aprofileCGH\u5bf9\u8c61<\/a>\u3002<\/p>\n\n\n\n<p>data(snijders)<\/p>\n\n\n\n<p># \u521b\u5efaprofileCGH\u5bf9\u8c61<\/p>\n\n\n\n<p>profileCGH &lt;- <a>as.profileCGH<\/a>(gm13330)<\/p>\n\n\n\n<p>\u63a5\u7740\uff0c\u6211\u4eec\u53ef\u4ee5<a>\u4f7f\u7528glad\u65b9\u6cd5\u5bf9\u7ec6\u80de\u7cfbgm13330\u8fdb\u884c\u5206<\/a>\u6790\uff0c\u5176\u4e2d\u5305\u62ec\u4e00\u7cfb\u5217\u53c2\u6570\u7684\u8bbe\u7f6e\uff0c\u5982\u5e73\u6ed1\u51fd\u6570\u3001\u5e26\u5bbd\u3001\u6a21\u578b\u3001\u6838\u51fd\u6570\u3001\u57fa\u7ebf\u8c03\u6574\u7b49\u3002<\/p>\n\n\n\n<p># \u4f7f\u7528GLAD\u51fd\u6570\u5bf9\u6570\u636e\u8fdb\u884c\u5904\u7406<\/p>\n\n\n\n<p>res &lt;- glad(profileCGH, mediancenter=FALSE,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;smoothfunc=&#8221;lawsglad&#8221;, bandwidth=10, round=1.5,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;model=&#8221;Gaussian&#8221;, lkern=&#8221;Exponential&#8221;, qlambda=0.999,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;base=FALSE,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;type=&#8221;tricubic&#8221;, param=c(d=6),<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;alpha=0.001, msize=2,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;method=&#8221;centroid&#8221;, nmax=8,<\/p>\n\n\n\n<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;verbose=FALSE)<\/p>\n\n\n\n<p>\u6700\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u52a0\u8f7d\u7ec6\u80de\u5e26\u6570\u636e\uff0c\u5e76\u7ed8\u5236\u5206\u6790\u7ed3\u679c\u56fe\u3002<\/p>\n\n\n\n<p>data(cytoband)<\/p>\n\n\n\n<p>plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, plotband=FALSE, Smoothing=&#8221;Smoothing&#8221;, cytoband = cytoband)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"354\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365714725_520FDA75-6569-4d51-9EEF-AEA88D367BA2.png?resize=554%2C354\" alt=\"\" class=\"wp-image-61764\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365714725_520FDA75-6569-4d51-9EEF-AEA88D367BA2.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365714725_520FDA75-6569-4d51-9EEF-AEA88D367BA2.png?resize=300%2C192 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u4e0a\u56fe\u4e2d\u5c55\u793a\u4e86\u7ec6\u80de\u7cfbgm13330\u7684DNA\u62f7\u8d1d\u6570\u53d8\u5f02\u5206\u6790\u7ed3\u679c\uff0c\u5177\u4f53\u89e3\u91ca\u5982\u4e0b\uff1a<\/p>\n\n\n\n<ol type=\"1\">\n<li>\u7eb5\u8f74\uff08log2\u6bd4\u503c\uff09\uff1a\u8868\u793aDNA\u62f7\u8d1d\u6570\u7684\u5bf9\u6570\u6bd4\u503c\u3002<\/li>\n\n\n\n<li>\u6a2a\u8f74\uff1a\u8868\u793a\u57fa\u56e0\u7ec4\u4f4d\u7f6e\u3002<\/li>\n\n\n\n<li>\u989c\u8272\u70b9\uff1a<ol><li>\u7ea2\u8272\u70b9\uff1a\u8868\u793a\u663e\u8457\u7684\u62f7\u8d1d\u6570\u589e\u52a0\uff08\u589e\u52a0\uff09\u3002<\/li><\/ol><ol><li>\u7eff\u8272\u70b9\uff1a\u8868\u793a\u663e\u8457\u7684\u62f7\u8d1d\u6570\u51cf\u5c11\uff08\u7f3a\u5931\uff09\u3002<\/li><\/ol>\n<ol>\n<li>\u9ec4\u8272\u70b9\uff1a\u8868\u793a\u6ca1\u6709\u663e\u8457\u53d8\u5316\u7684\u533a\u57df\u3002\uff08\u6b63\u5e38\uff09<\/li>\n<\/ol>\n<\/li>\n\n\n\n<li>\u9ed1\u8272\u7ebf\u6761\uff1a\u8868\u793a\u5e73\u6ed1\u540e\u7684\u62f7\u8d1d\u6570\u53d8\u5f02\u8d8b\u52bf\u3002<\/li>\n\n\n\n<li>\u7ea2\u8272\u865a\u7ebf\uff1a\u8868\u793a\u65ad\u70b9\u4f4d\u7f6e\u3002<\/li>\n<\/ol>\n\n\n\n<p>\u901a\u8fc7\u8fd9\u4e9b\u4fe1\u606f\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u770b\u5230\u57fa\u56e0\u7ec4\u4e2d\u54ea\u4e9b\u533a\u57df\u5b58\u5728\u663e\u8457\u7684\u62f7\u8d1d\u6570\u53d8\u5f02\uff0c\u8fd9\u5bf9\u4e8e\u7406\u89e3\u57fa\u56e0\u7ec4\u7ed3\u6784\u53d8\u5f02\u548c\u76f8\u5173\u75be\u75c5\u7814\u7a76\u5177\u6709\u91cd\u8981\u610f\u4e49\u3002<\/p>\n\n\n\n<ul>\n<li>daglad\u51fd\u6570<\/li>\n<\/ul>\n\n\n\n<p>daglad\u51fd\u6570\u7684\u4f7f\u7528\u65b9\u6cd5\u57fa\u672c\u548cglad\u4e00\u81f4\u54e6\uff0c\u8ba9\u6211\u4eec\u5feb\u901f\u8fc7\u4e00\u904d\u5427\uff01\u6211\u4eec\u5148\u52a0\u8f7d\u6765\u81eaVeltman \u7b49\u4eba (2003) \u7684\u6570\u636e\uff0c\u5176\u4e2d\u5305\u62ec\u4e24\u4e2a\u9635\u5217 CGH \u8c31\u3002<\/p>\n\n\n\n<p>data(veltman)<\/p>\n\n\n\n<p>profileCGH &lt;- as.profileCGH(P9)<\/p>\n\n\n\n<p>profileCGH&nbsp;&lt;-&nbsp;daglad(profileCGH,mediancenter=FALSE,normalrefcenter=FALSE, genomestep=FALSE,smoothfunc=&#8221;lawsglad&#8221;,lkern=&#8221;Exponential&#8221;,model=&#8221;Gaussian&#8221;,&nbsp;qlambda=0.999, bandwidth=10, base=FALSE, round=1.5,&nbsp;lambdabreak=8, lambdaclusterGen=40, param=c(d=6), alpha=0.001, msize=2,&nbsp;method=&#8221;centroid&#8221;, nmin=1, nmax=8,&nbsp;amplicon=1, deletion=-5,deltaN=0.2,forceGL=c(-0.3,0.3),nbsigma=3,MinBkpWeight=0.35, CheckBkpPos=TRUE)<\/p>\n\n\n\n<p># \u7ed8\u5236\u7ed3\u679c\u56fe<\/p>\n\n\n\n<p>plotProfile(profileCGH, Smoothing=&#8221;Smoothing&#8221;, Bkp=TRUE, plotband=FALSE, cytoband = cytoband)<\/p>\n\n\n\n<p>abline(h=c(-0.3,-0.2,0.2,0.3),col=c(&#8220;green&#8221;,&#8221;black&#8221;,&#8221;black&#8221;,&#8221;red&#8221;))<\/p>\n\n\n\n<p>axis(2,at=c(-0.3,-0.2,0.2,0.3), labels=c(&#8220;forceGL[1]&#8221;,&#8221;-deltaN&#8221;,&#8221;+deltaN&#8221;,&#8221;forceGL[2]&#8221;), las=2)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"340\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365725577_F8AE6896-4AC4-4869-9CBA-56E3F52BE3B9.png?resize=554%2C340\" alt=\"\" class=\"wp-image-61765\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365725577_F8AE6896-4AC4-4869-9CBA-56E3F52BE3B9.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365725577_F8AE6896-4AC4-4869-9CBA-56E3F52BE3B9.png?resize=300%2C184 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff0cdaglad \u51fd\u6570\u5141\u8bb8\u9009\u62e9\u4e00\u4e9b\u9608\u503c\u6765\u5e2e\u52a9\u7b97\u6cd5\u8bc6\u522b\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u72b6\u6001\u3002\u9608\u503c\u5728\u4ee5\u4e0b\u53c2\u6570\u4e2d\u7ed9\u51fa\uff1adeltaN\u3001forceGL\u3001deletion\u3001amplicon\u3002\u6211\u4eec\u53ef\u4ee5\u4fee\u6539\u4e00\u4e0b\u53c2\u6570\uff0c\u6bd4\u8f83\u4e00\u4e0b\u4e0d\u540c\u53c2\u6570\u5bf9\u7ed3\u679c\u7684\u5f71\u54cd\u3002\u8ba9\u6211\u4eec\u628adeltaN\u4ece0.2\u6539\u52300.1\uff0cdeltaN\u4ecec(-0.3,0.3)\u6539\u5230c(-0.15,0.15)\uff0c\u770b\u4e00\u4e0b\u7ed3\u679c\u4f1a\u6709\u4ec0\u4e48\u53d8\u5316\u5427\uff01<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"348\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365736276_DDD192C2-117D-49e6-ADAD-25B045E07485.png?resize=554%2C348\" alt=\"\" class=\"wp-image-61766\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365736276_DDD192C2-117D-49e6-ADAD-25B045E07485.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365736276_DDD192C2-117D-49e6-ADAD-25B045E07485.png?resize=300%2C188 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u901a\u8fc7\u6bd4\u8f83\u8c03\u6574\u524d\u540e\u7684\u7ed3\u679c\u56fe\uff0c\u53ef\u4ee5\u66f4\u6e05\u695a\u5730\u4e86\u89e3\u4e0d\u540c\u9608\u503c\u5bf9\u4e8e\u7b97\u6cd5\u7ed3\u679c\u7684\u5f71\u54cd\uff0c\u4ee5\u786e\u5b9a\u6700\u9002\u5408\u6570\u636e\u96c6\u7684\u53c2\u6570\u8bbe\u7f6e\u3002\u8fd9\u79cd\u5206\u6790\u6709\u52a9\u4e8e\u4f18\u5316\u7b97\u6cd5\u7684\u6027\u80fd\uff0c\u5e76\u63d0\u9ad8\u5bf9\u57fa\u56e0\u7ec4\u53d8\u5f02\u7684\u8bc6\u522b\u80fd\u529b\u3002<\/p>\n\n\n\n<p>\u5728daglad\u51fd\u6570\u4e2d\uff0c\u5982\u679c\u8bbe\u7f6e\u4e86`genestep=TRUE`\uff0c\u5219\u4f1a\u5bf9\u6574\u4e2a\u57fa\u56e0\u7ec4\u8fdb\u884c\u5e73\u6ed1\u5904\u7406\uff0c\u8fde\u63a5\u6240\u6709\u67d3\u8272\u4f53\u8fdb\u884c\u5904\u7406\u3002\u7b97\u6cd5\u4f1a\u8bc6\u522b\u4e0e\u6b63\u5e38DNA\u6c34\u5e73\u76f8\u5bf9\u5e94\u7684\u7c07\uff0c\u7136\u540e\u5c06\u9608\u503c\u4e0e\u8fd9\u4e9b\u7c07\u7684\u4e2d\u4f4d\u6570\u8fdb\u884c\u6bd4\u8f83\u3002\u8fd9\u5c31\u53ef\u4ee5\u6839\u636e\u6574\u4e2a\u57fa\u56e0\u7ec4\u6570\u636e\u7684\u5168\u8c8c\u6765\u8c03\u6574\u9608\u503c\uff0c\u4ee5\u786e\u4fdd\u6211\u4eec\u8bc6\u522b\u7684\u53d8\u5f02\u533a\u57df\u5728\u6574\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u662f\u663e\u773c\u7684\uff0c\u6709\u52a9\u4e8e\u63d0\u9ad8\u6211\u4eec\u7b97\u6cd5\u7684\u51c6\u786e\u6027\u548c\u53ef\u9760\u6027\u3002<\/p>\n\n\n\n<ul>\n<li>\u53c2\u6570\u7684\u8c03\u6574<\/li>\n<\/ul>\n\n\n\n<p>\u5728\u4e0a\u8ff0\u51fd\u6570\u4e2d\uff0c\u6bd4\u8f83\u91cd\u8981\u7684\u4e00\u4e9b\u53c2\u6570\u662f`lambdabreak`\u3001`lambdacluster`\u3001`lambdaclusterGen`\u548c`param`\u53c2\u6570\u3002\u901a\u8fc7\u8c03\u6574\u8fd9\u4e9b\u53c2\u6570\uff0c\u53ef\u4ee5\u5f71\u54cd\u7b97\u6cd5\u68c0\u6d4b\u65ad\u70b9\u7684\u6570\u91cf\u3002<\/p>\n\n\n\n<ol type=\"1\">\n<li>`lambdabreak`\u53c2\u6570\u63a7\u5236\u4e86\u7b97\u6cd5\u4e2d\u7528\u4e8e\u8bc6\u522b\u65ad\u70b9\u7684\u60e9\u7f5a\u529b\u5ea6\uff0c\u8f83\u5c0f\u7684\u503c\u4f1a\u5bfc\u81f4\u66f4\u591a\u7684\u65ad\u70b9\u88ab\u68c0\u6d4b\u51fa\u6765\u3002<\/li>\n\n\n\n<li>`lambdacluster`\u548c`lambdaclusterGen`\u53c2\u6570\u5219\u7528\u4e8e\u63a7\u5236\u7c07\uff08cluster\uff09\u7684\u8bc6\u522b\uff0c\u8f83\u5c0f\u7684\u503c\u53ef\u80fd\u4f1a\u5bfc\u81f4\u66f4\u591a\u7684\u7c07\u88ab\u8bc6\u522b\u51fa\u6765\u3002<\/li>\n\n\n\n<li>`param`\u53c2\u6570\u4e2d\u7684`d`\u503c\u4e5f\u4f1a\u5f71\u54cd\u7b97\u6cd5\u68c0\u6d4b\u65ad\u70b9\u7684\u6570\u91cf\uff0c\u8f83\u5c0f\u7684`d`\u503c\u53ef\u80fd\u4f1a\u5bfc\u81f4\u66f4\u591a\u7684\u65ad\u70b9\u88ab\u68c0\u6d4b\u51fa\u6765\u3002<\/li>\n<\/ol>\n\n\n\n<p>\u9488\u5bf9\u4fe1\u566a\u6bd4\u975e\u5e38\u5c0f\u7684\u9635\u5217\u5b9e\u9a8c\uff0c\u5efa\u8bae\u964d\u4f4e\u4e0a\u8ff0\u53c2\u6570\u7684\u503c\uff0c\u7279\u522b\u662f\u5c06`param`\u53c2\u6570\u4e2d\u7684`d`\u503c\u8c03\u6574\u4e3a3\u6216\u66f4\u5c0f\u3002\u8fd9\u662f\u56e0\u4e3a\u5728\u4fe1\u566a\u6bd4\u8f83\u5c0f\u7684\u60c5\u51b5\u4e0b\uff0c\u5bf9\u7ec6\u5fae\u7684\u53d8\u5316\u66f4\u4e3a\u654f\u611f\uff0c\u56e0\u6b64\u964d\u4f4e\u53c2\u6570\u503c\u53ef\u4ee5\u5e2e\u52a9\u7b97\u6cd5\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\u66f4\u597d\u5730\u8bc6\u522b\u51fa\u6f5c\u5728\u7684\u65ad\u70b9\uff0c\u4ece\u800c\u63d0\u9ad8\u5bf9\u53d8\u5f02\u7684\u68c0\u6d4b\u80fd\u529b\u3002<\/p>\n\n\n\n<ul>\n<li>\u56fe\u5f62\u51fd\u6570<\/li>\n<\/ul>\n\n\n\n<p>arrayPlot\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u51fa\u9635\u5217 CGH \u7684\u7a7a\u95f4\u56fe\u50cf\uff0c\u4f1a\u663e\u793a\u4e0d\u540c\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u4fe1\u53f7\u5f3a\u5ea6\u6bd4\u503c\uff0c\u4ee5\u4fbf\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u89c2\u5bdf\u57fa\u56e0\u7ec4\u7684\u62f7\u8d1d\u6570\u53d8\u5f02\u7b49\u4fe1\u606f\u3002<\/p>\n\n\n\n<p>data(arrayCGH)<\/p>\n\n\n\n<p># object of class arrayCGH<\/p>\n\n\n\n<p>array &lt;- list(arrayValues=array2, arrayDesign=c(4,4,21,22))<\/p>\n\n\n\n<p>class(array) &lt;- &#8220;arrayCGH&#8221;<\/p>\n\n\n\n<p><a><\/a>arrayPlot(array,&#8221;Log2Rat&#8221;, bar=&#8221;none&#8221;)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"298\" height=\"254\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365746492_9FF3CFD5-5053-430a-90C3-797789ED8722.png?resize=298%2C254\" alt=\"\" class=\"wp-image-61767\" data-recalc-dims=\"1\"\/><\/figure>\n\n\n\n<p>arrayPersp\u51fd\u6570\u53ef\u4ee5\u7ed8\u5236\u9635\u5217 CGH \u4e09\u7ef4\u900f\u89c6\u56fe\uff0c\u5c55\u793a\u4e86\u9635\u5217\u6bd4\u8f83\u6742\u4ea4\u6570\u636e\u5728\u7a7a\u95f4\u4e2d\u7684\u5206\u5e03\u60c5\u51b5\u3002\u901a\u8fc7\u900f\u89c6\u56fe\uff0c\u53ef\u4ee5\u66f4\u76f4\u89c2\u5730\u89c2\u5bdf\u57fa\u56e0\u7ec4\u7684\u62f7\u8d1d\u6570\u53d8\u5f02\u3001\u6570\u636e\u7684\u5206\u5e03\u89c4\u5f8b\u4ee5\u53ca\u4e0d\u540c\u533a\u57df\u4e4b\u95f4\u7684\u76f8\u5bf9\u4fe1\u53f7\u5f3a\u5ea6\u7b49\u4fe1\u606f\u3002<\/p>\n\n\n\n<p>arrayPersp(array,&#8221;Log2Rat&#8221;, box=FALSE, theta=110, phi=40, bar=FALSE)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"437\" height=\"398\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365756588_85F9FFDE-9073-4f2b-9DFE-C7EC657E1163.png?resize=437%2C398\" alt=\"\" class=\"wp-image-61768\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365756588_85F9FFDE-9073-4f2b-9DFE-C7EC657E1163.png?w=437 437w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365756588_85F9FFDE-9073-4f2b-9DFE-C7EC657E1163.png?resize=300%2C273 300w\" sizes=\"(max-width: 437px) 100vw, 437px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u53e6\u5916\u8fd8\u6709\u4e00\u4e2a\u6211\u4eec\u5df2\u7ecf\u8ba4\u8bc6\u7684\u8001\u670b\u53cb\u2014\u2014plotProfile\u51fd\u6570\uff0c\u5728\u4e0a\u9762\u4ecb\u7ecdglad\u51fd\u6570\u65f6\uff0c\u6211\u4eec\u5c31\u5df2\u7ecf\u4f7f\u7528\u8fc7\u5b83\u6765\u7ed8\u5236\u6574\u4e2a<a>\u57fa\u56e0\u7ec4\u7684\u56fe\u8c31<\/a>\u3002\u5982\u679c\u60f3\u8981\u5728\u56fe\u4e2d\u540c\u65f6\u5c55\u793a\u7ec6\u80de\u9057\u4f20\u5e26\uff0c\u53ef\u4ee5\u5c06plotband\u53c2\u6570\u8bbe\u7f6e\u4e3aTRUE\uff08\u9ed8\u8ba4\u503c\uff09\u54e6~<\/p>\n\n\n\n<p>plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing=&#8221;Smoothing&#8221;,plotband=TRUE, cytoband = cytoband)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"375\" height=\"237\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365766424_19489C86-A10A-4d56-9CCF-025B54CA2C32.png?resize=375%2C237\" alt=\"\" class=\"wp-image-61769\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365766424_19489C86-A10A-4d56-9CCF-025B54CA2C32.png?w=375 375w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365766424_19489C86-A10A-4d56-9CCF-025B54CA2C32.png?resize=300%2C190 300w\" sizes=\"(max-width: 375px) 100vw, 375px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u9664\u6b64\u4e4b\u5916\uff0c\u8fd8\u53ef\u4ee5\u7528\u5b83\u6765\u7ed8\u5236<a>1\u53f7\u67d3\u8272\u4f53\u7684\u57fa\u56e0\u7ec4\u56fe\u8c31\u548c\u5e26\u6807\u7b7e\u7684\u7ec6\u80de\u9057\u4f20\u5e26<\/a>\uff0c\u82e5\u4e0d\u60f3\u540c\u65f6\u7ed8\u5236\u7ec6\u80de\u9057\u4f20\u5e26\uff0c\u53ef\u4ee5\u5c06plotband\u53c2\u6570\u8bbe\u4e3aFALSE\u54e6~<\/p>\n\n\n\n<p>text &lt;- list(x=c(90000,200000),y=c(0.15,0.3),labels=c(&#8220;NORMAL&#8221;,&#8221;GAIN&#8221;), cex=2)<\/p>\n\n\n\n<p>plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,<\/p>\n\n\n\n<p>Smoothing=&#8221;Smoothing&#8221;, text=text, cytoband = cytoband)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"387\" height=\"271\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365777801_E15120FE-05E9-4e57-BE2C-269AFF272AC2.png?resize=387%2C271\" alt=\"\" class=\"wp-image-61770\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365777801_E15120FE-05E9-4e57-BE2C-269AFF272AC2.png?w=387 387w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730365777801_E15120FE-05E9-4e57-BE2C-269AFF272AC2.png?resize=300%2C210 300w\" sizes=\"(max-width: 387px) 100vw, 387px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5728\u8fd9\u5f20\u56fe\u4e2d\uff0c&#8221;NORMAL&#8221;\u8868\u793a\u67d3\u8272\u4f53\u4e0a\u6b63\u5e38\u533a\u57df\uff0c\u6ca1\u6709\u53d8\u5f02\uff0c\u751f\u7269\u7279\u5f81\u6b63\u5e38\u3002\u800c&#8221;GAIN&#8221;\u8868\u793a\u57fa\u56e0\u7ec4\u53d1\u751f\u53d8\u5f02\u5bfc\u81f4DNA\u62f7\u8d1d\u6570\u589e\u52a0\u7684\u533a\u57df\u3002\u5728\u8fd9\u4e9b\u533a\u57df\uff0c\u53ef\u80fd\u5b58\u5728\u989d\u5916\u7684\u57fa\u56e0\u62f7\u8d1d\u6216\u5176\u4ed6\u57fa\u56e0\u7ec4\u7a81\u53d8\uff0c\u5bfc\u81f4\u8be5\u533a\u57df\u7684\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u589e\u52a0\u3002\u8fd9\u53ef\u80fd\u4e0e\u80bf\u7624\u53d1\u5c55\u3001\u7ec6\u80de\u589e\u6b96\u7b49\u75be\u75c5\u76f8\u5173\uff0c\u56e0\u6b64\u5bf9&#8221;GAIN&#8221;\u533a\u57df\u7684\u5206\u6790\u53ef\u4ee5\u5e2e\u52a9\u7814\u7a76\u76f8\u5173\u75be\u75c5\u7684\u53d1\u75c5\u673a\u5236\u548c\u6cbb\u7597\u7b56\u7565\u3002<\/p>\n\n\n\n<p>\u4f19\u4f34\u4eec\uff0c\u5c0f\u679c\u5df2\u7ecf\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b8c\u6210\u4e86GLAD\u7684\u521d\u6b65\u63a2\u7d22\u3002\u73b0\u5728\uff0c\u4f60\u53ef\u4ee5\u5f00\u59cb\u81ea\u5df1\u52a8\u624b\uff0c\u5229\u7528GLAD\u5305\u6765\u5206\u6790\u9635\u5217CGH\u6570\u636e\u5566\uff0c\u5305\u62ec\u5bfb\u627e\u57fa\u56e0\u7ec4\u7684\u65ad\u70b9\u3001\u786e\u5b9a\u67d3\u8272\u4f53\u533a\u57df\u7684\u72b6\u6001\u7b49\u3002\u4f7f\u7528\u65f6\u8bb0\u5f97\u5145\u5206\u5229\u7528GLAD\u63d0\u4f9b\u7684\u56fe\u5f62\u51fd\u6570\u54e6\uff0c\u53ef\u4ee5\u8ba9\u4f60\u7684\u5206\u6790\u8fc7\u7a0b\u4e8b\u534a\u529f\u500d\uff01<\/p>\n\n\n\n<p>\u65e0\u8bba\u4f60\u662f\u5728\u4f18\u5316\u4ee3\u7801\uff0c\u8fd8\u662f\u5728\u4e91\u7aef\u8fdb\u884c\u4fbf\u6377\u7684\u5206\u6790\uff0c\u4e91\u751f\u4fe1\u795e\u5668\u90fd\u80fd\u4e3a\u4f60\u63d0\u4f9b\u5f3a\u5927\u7684\u652f\u6301\u3002<strong>\u6b22\u8fce<\/strong><strong>\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u795e\u5668<\/strong><strong>\uff0c<\/strong><strong>\u53ea\u9700<\/strong><strong>\u4e00\u952e<\/strong><strong>\u4e0a\u4f20\u6570\u636e\uff0c\u60f3\u8981\u7684\u56fe\u5c31\u80fd\u8f7b\u677e<\/strong><strong>get~<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/strong><a href=\"http:\/\/www.biocloudservice.com\/home.html\"><strong>http:\/\/www.biocloudservice.com\/home.html<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u563f\u670b\u53cb\u4eec\uff0c\u5c0f\u679c\u5411\u5bfc\u53c8\u6765\u5566\uff0c\u6b22\u8fce\u6765\u5230\u751f\u7269\u4fe1\u606f\u5b66\u7684\u5947\u5999\u4e16\u754c\u3002\u4eca\u5929\uff0c\u6211\u4eec\u8981\u4e00\u8d77\u8e0f\u4e0a\u4e00\u573a\u9635\u5217CGH\uff08\u6bd4\u8f83\u57fa\u56e0\u7ec4\u6742\u4ea4\uff09\u6570 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/61763"}],"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=61763"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61763\/revisions"}],"predecessor-version":[{"id":61771,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61763\/revisions\/61771"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61763"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61763"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61763"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}