{"id":61085,"date":"2024-10-17T09:54:58","date_gmt":"2024-10-17T01:54:58","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61085"},"modified":"2024-10-17T09:54:58","modified_gmt":"2024-10-17T01:54:58","slug":"%e7%94%9f%e4%bf%a1%e5%bf%85%e5%a4%87%ef%bc%81cindex%e5%8c%85%ef%bc%8c%e5%b8%a6%e4%bd%a0%e8%bd%bb%e6%9d%be%e9%87%8f%e5%8c%96%e6%9f%93%e8%89%b2%e4%bd%93%e4%b8%8d%e7%a8%b3%e5%ae%9a%e6%80%a7%e3%80%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61085","title":{"rendered":"\u751f\u4fe1\u5fc5\u5907\uff01CINdex\u5305\uff0c\u5e26\u4f60\u8f7b\u677e\u91cf\u5316\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u3001\u5206\u6790\u57fa\u56e0\u6269\u589e\u548c\u7f3a\u5931\uff01"},"content":{"rendered":"\n

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u5927\u5bb6\u597d\uff01\u4eca\u5929\u5927\u6d77\u54e5\u8981\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u5728\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u7814\u7a76\u9886\u57df\u4e2d\u4e0d\u53ef\u6216\u7f3a\u7684R\u5305\u2014\u2014CINdex\u5305\uff01CINdex\u5305\u662f\u4e13\u95e8\u7528\u4e8e\u5206\u6790\u548c\u91cf\u5316\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u7684\u5f3a\u5927\u5de5\u5177\u3002\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\uff08Chromosomal Instability, CIN\uff09\u662f\u6307\u67d3\u8272\u4f53\u7ed3\u6784\u6216\u6570\u76ee\u53d1\u751f\u5f02\u5e38\u53d8\u5316\u7684\u73b0\u8c61\uff0c\u5e38\u89c1\u4e8e\u764c\u75c7\u7ec6\u80de\u4e2d\uff0c\u5bf9\u80bf\u7624\u7684\u53d1\u751f\u3001\u53d1\u5c55\u53ca\u6cbb\u7597\u6709\u91cd\u8981\u5f71\u54cd\u3002CINdex\u5305\u63d0\u4f9b\u4e86\u591a\u79cd\u529f\u80fd\u5f3a\u5927\u7684\u51fd\u6570\uff0c\u80fd\u591f\u5e2e\u52a9\u6211\u4eec\u6df1\u5165\u7406\u89e3\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u6a21\u5f0f\uff0c\u8bc6\u522b\u57fa\u56e0\u7ec4\u4e2d\u7684\u6269\u589e\u6216\u7f3a\u5931\u533a\u57df\uff0c\u5e76\u63a2\u7d22\u8fd9\u4e9b\u53d8\u5f02\u4e0e\u4e34\u5e8a\u7279\u5f81\u4e4b\u95f4\u7684\u5173\u7cfb\u3002\u5927\u6d77\u54e5\u53ef\u662f\u5389\u5bb3\u7684\u751f\u4fe1\u9ad8\u624b\uff0c\u8981\u662f\u540c\u5b66\u4eec\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\uff01\uff01\uff01<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u672c\u6b21\u5b66\u4e60\u4e2d\uff0c\u6211\u4eec\u4e0d\u4ec5\u5c06\u5b66\u4f1a\u5982\u4f55\u5b89\u88c5\u548c\u4f7f\u7528CINdex\u5305\uff0c\u8fd8\u5c06\u638c\u63e1\u57fa\u56e0\u7ec4\u6570\u636e\u7684\u9884\u5904\u7406\u3001\u67d3\u8272\u4f53\u7a33\u5b9a\u6027\u5206\u6790\u3001\u4ee5\u53ca\u7ed3\u679c\u7684\u53ef\u89c6\u5316\u65b9\u6cd5\u3002\u901a\u8fc7\u5b9e\u9645\u793a\u4f8b\u7684\u6f14\u793a\uff0c\u6211\u4eec\u5c06\u66f4\u6df1\u5165\u5730\u7406\u89e3\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u5728\u80bf\u7624\u53d1\u751f\u548c\u53d1\u5c55\u4e2d\u7684\u4f5c\u7528\uff0c\u5e76\u63a2\u7d22\u5176\u6f5c\u5728\u7684\u751f\u7269\u5b66\u673a\u5236\u3002\u6211\u76f8\u4fe1\uff0c\u901a\u8fc7\u4eca\u5929\u7684\u5b66\u4e60\uff0c\u540c\u5b66\u4eec\u90fd\u80fd\u591f\u66f4\u52a0\u719f\u7ec3\u5730\u5e94\u7528CINdex\u5305\uff0c\u4e3a\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u548c\u80bf\u7624\u7814\u7a76\u7684\u8fdb\u6b65\u8d21\u732e\u81ea\u5df1\u7684\u4e00\u4efd\u529b\u91cf\uff01\u63a5\u4e0b\u6765\uff0c\u5c31\u8ba9\u6211\u4eec\u6b63\u5f0f\u5f00\u542f\u5bf9CINdex\u5305\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01<\/p>\n\n\n\n

\u672c\u6b21\u4ecb\u7ecd\u7684<\/strong>R\u5305<\/strong>\u9700\u8981\u8f83\u591a\u7684\u786c\u4ef6\u8d44\u6e90\uff0c\u5728<\/strong>\u670d\u52a1\u5668<\/strong>\u53ef\u4ee5\u66f4\u52a0\u6d41\u7545<\/strong>\u8fd0\u884c\uff0c<\/strong>\u540c\u5b66\u4eec<\/strong>\u5982\u679c\u6ca1\u6709\u81ea\u5df1\u7684\u670d\u52a1\u5668\u6b22\u8fce\u8054\u7cfb\u6211\u4eec\u4f7f\u7528\u670d\u52a1\u5668\u79df\u8d41~<\/strong><\/strong><\/p>\n\n\n\n

CINdex\u5305\u4ecb\u7ecd<\/p>\n\n\n\n

CINdex\u5305\u662f\u4e00\u4e2a\u4e13\u4e3a\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u7814\u7a76\u8bbe\u8ba1\u7684R\u8bed\u8a00\u5de5\u5177\uff0c\u65e8\u5728\u5206\u6790\u548c\u91cf\u5316\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u3002\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u662f\u6307\u67d3\u8272\u4f53\u7ed3\u6784\u6216\u6570\u76ee\u5f02\u5e38\u53d8\u5316\u7684\u73b0\u8c61\uff0c\u5e38\u89c1\u4e8e\u764c\u75c7\u7ec6\u80de\u4e2d\uff0c\u5bf9\u80bf\u7624\u7684\u53d1\u751f\u3001\u53d1\u5c55\u53ca\u6cbb\u7597\u53cd\u5e94\u6709\u91cd\u8981\u5f71\u54cd\u3002CINdex\u5305\u63d0\u4f9b\u4e86\u591a\u79cd\u529f\u80fd\u5f3a\u5927\u7684\u51fd\u6570\uff0c\u5e2e\u52a9\u7814\u7a76\u4eba\u5458\u6df1\u5165\u7406\u89e3\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u6a21\u5f0f\uff0c\u8bc6\u522b\u57fa\u56e0\u7ec4\u4e2d\u7684\u6269\u589e\u6216\u7f3a\u5931\u533a\u57df\uff0c\u5e76\u63a2\u7d22\u8fd9\u4e9b\u53d8\u5f02\u4e0e\u4e34\u5e8a\u7279\u5f81\u4e4b\u95f4\u7684\u5173\u7cfb\u3002<\/p>\n\n\n\n

CINdex\u5305\u5b89\u88c5<\/p>\n\n\n\n

\u9700\u8981R\u8bed\u8a00\u7248\u672c\u4e3a4.4\uff0c\u5728\u63a7\u5236\u53f0\u4e2d\u8f93\u5165\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n\n\n\n

if (!require(“BiocManager”, quietly = TRUE))<\/p>\n\n\n\n

    install.packages(“BiocManager “)<\/p>\n\n\n\n

BiocManager::install(“CINdex”) # \u5728BiocManager\u73af\u5883\u4e0b\u5b89\u88c5CINdex<\/p>\n\n\n\n

\u67e5\u770b\u662f\u5426\u5b89\u88c5\u6210\u529f\uff1a<\/p>\n\n\n\n

packageVersion(“CINdex”) # \u67e5\u770bCINdex\u7248\u672c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u663e\u793a\u4e3a1.32.0\u7248\u672c\uff0c\u5219\u8868\u793a\u5df2\u7ecf\u5b89\u88c5\u4e86CINdex\u5305\u3002<\/p>\n\n\n\n

\u5206\u6790\u524d\u6570\u636e\u51c6\u5907<\/p>\n\n\n\n

\u8f7d\u5165\u9700\u8981\u7684\u5305\u548c\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u8f7d\u5165\u9700\u8981\u7528\u5230\u7684\u5305\u548c\u6570\u636e\uff0c\u5728\u672c\u6587\u4e2d\u6211\u4eec\u5c06\u4f7f\u7528CINdex\u5305\u81ea\u5e26\u7684\u793a\u4f8b\u6570\u636e\uff08\u201cgrl.data\u201d\uff09\u6765\u6f14\u793aCINdex\u5305\u7684\u529f\u80fd\uff0c\u56e0\u6b64\u6211\u4eec\u53ea\u9700\u8981\u8f7d\u5165CINdex\u5305\u5e76\u5bfc\u5165\u201cgrl.data\u201d\u5373\u53ef\uff0c\u76f8\u5173\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

library(CINdex) #\u8f7d\u5165CINdex\u5305<\/p>\n\n\n\n

data(“grl.data”) #\u5bfc\u5165grl.data\u6570\u636e<\/p>\n\n\n\n

grl.data #\u67e5\u770bgrl.data\u6570\u636e\u4fe1\u606f<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u53ef\u77e5grl.data\u5305\u542b22\u4e2a\u67d3\u8272\u4f53\u4e0a1318\u4e2a\u57fa\u56e0\u5206\u6bb5\u7684\u6570\u636e\uff0c\u5728\u540e\u7eed\u5bf9\u4e8e\u5355\u4e2a\u67d3\u8272\u4f53\u5206\u6790\u65f6\uff0c\u8fd8\u9700\u8981\u7528\u5230\u63a2\u9488\u6ce8\u91ca\u548c\u53c2\u8003\u6ce8\u91ca\u6587\u4ef6\uff0c\u4ee5\u53ca\u4e34\u5e8a\u6570\u636e\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u53ef\u4ee5\u63d0\u524d\u8f7d\u5165\uff0c\u76f8\u5173\u7684\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

data(“cnvgr.18.auto”) #\u8f7d\u5165\u63a2\u9488\u6ce8\u91ca\u6587\u4ef6<\/p>\n\n\n\n

data(“snpgr.18.auto”) #\u8f7d\u5165\u63a2\u9488\u6ce8\u91ca\u6587\u4ef6<\/p>\n\n\n\n

data(“hg18.ucsctrack”) #\u8f7d\u5165\u53c2\u8003\u6ce8\u91ca\u6587\u4ef6<\/p>\n\n\n\n

data(“clin.crc”) #\u8f7d\u5165\u4e34\u5e8a\u6570\u636e<\/p>\n\n\n\n

\u4f7f\u7528CINdex\u5305\u5206\u6790\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027<\/p>\n\n\n\n

\u5206\u6790\u6240\u6709<\/strong>\u67d3\u8272\u4f53<\/strong>\u7684\u4e0d\u7a33\u5b9a\u6027<\/strong><\/strong><\/p>\n\n\n\n

\u81f3\u6b64\uff0c\u6211\u4eec\u5df2\u7ecf\u8f7d\u5165\u4e86\u9700\u8981\u7528\u5230\u7684\u5305\u548c\u6570\u636e\uff0c\u63a5\u4e0b\u6765\uff0c\u8ba9\u6211\u4eec\u8c03\u7528run.cin.chr()\u51fd\u6570\u5206\u6790\u4e00\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u6240\u6709\u67d3\u8272\u4f53\u7684\u4e0d\u7a33\u5b9a\u6027\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

run.cin.chr(grl.seg = grl.data) # \u8fd0\u884crun.cin.chr\u51fd\u6570\u8ba1\u7b97\u67d3\u8272\u4f53\u7ea7\u522b\u7684\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u6307\u6570\uff08CIN\uff09<\/p>\n\n\n\n

\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u5728\u6b64\u793a\u4f8b\u4e2d\uff0c\u6b64\u51fd\u6570\u53c2\u6570\u5747\u4fdd\u6301\u9ed8\u8ba4\u3002<\/p>\n\n\n\n

\u8be5\u4ee3\u7801\u5c06\u8ba1\u7b97\u4ee5\u4e0b\u9ed8\u8ba4\u8bbe\u7f6e\u7684\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\uff1a<\/p>\n\n\n\n

– \u6269\u589e\u9608\u503c\u4e3a2.5\u548c\u635f\u5931\u9608\u503c\u4e3a1.5<\/p>\n\n\n\n

– \u6269\u589e\u9608\u503c\u4e3a2.25\u548c\u635f\u5931\u9608\u503c\u4e3a1.75<\/p>\n\n\n\n

– \u6269\u589e\u9608\u503c\u4e3a2.10\u548c\u635f\u5931\u9608\u503c\u4e3a1.90<\/p>\n\n\n\n

\u5bf9\u4e8e\u6bcf\u4e2a\u9608\u503c\u8bbe\u7f6e\uff0c\u6b64\u51fd\u6570\u5c06\u8ba1\u7b97\u6269\u589e\u3001\u635f\u5931\u548c\u6269\u589e\u4e0e\u635f\u5931\u7ec4\u5408\uff08\u79f0\u4e3a\u201csum\u201d\uff09\u7684\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u3002\u5e76\u4e14\u5bf9\u4e8e\u4e0a\u8ff0\u8bbe\u7f6e\u7684\u6bcf\u79cd\u60c5\u51b5\u4e0b\uff0c\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u5747\u5206\u522b\u4f7f\u7528\u5f52\u4e00\u5316\u548c\u4e0d\u5f52\u4e00\u5316\u8fdb\u884c\u8ba1\u7b97\u3002<\/p>\n\n\n\n

\u56e0\u6b64\uff0c\u5728\u51fd\u6570\u7ed3\u675f\u65f6\uff0c\u5c06\u5728\u201coutput chr\u201d\u6587\u4ef6\u5939\u4e2d\u521b\u5efa18\u4e2a\u6587\u4ef6\uff0c\u6bcf\u4e00\u4e2a\u6587\u4ef6\u540d\u5747\u4ee5\u53c2\u6570\u8bbe\u7f6e\u547d\u540d\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u53ef\u4ee5\u8c03\u7528comp.heatmap()\u51fd\u6570\u6765\u7ed8\u5236\u67d3\u8272\u4f53\u6c34\u5e73\u7ed3\u679c\u7684\u70ed\u56fe\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

comp.heatmap(R_or_C=”Regular”, clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, in.folder.name=”output_chr_cin”, out.folder.name=”output_chr_plots”) # \u751f\u6210\u67d3\u8272\u4f53\u7ea7\u522b\u7684CIN\u6307\u6570\u70ed\u56fe\uff0cR_or_C\u53c2\u6570\u4e3a”Regular”\uff0c\u8868\u793a\u4f7f\u7528\u6807\u51c6\u7684\u67d3\u8272\u4f53\u7f16\u53f7\uff0cclinical.inf\u53c2\u6570\u4e3a\u4e34\u5e8a\u4fe1\u606f\uff0c\u5305\u542b\u6837\u672c\u7684\u4e34\u5e8a\u7279\u5f81\uff0cgenome.ucsc\u53c2\u6570\u4e3a\u53c2\u8003\u57fa\u56e0\u7ec4\u6ce8\u91ca\uff0cin.folder.name\u53c2\u6570\u6307\u5b9a\u8f93\u5165\u6570\u636e\u6587\u4ef6\u5939\u540d\u79f0\uff0cout.folder.name\u53c2\u6570\u6307\u5b9a\u8f93\u51fa\u56fe\u7247\u6587\u4ef6\u5939\u540d\u79f0<\/p>\n\n\n\n

\u8be5\u51fd\u6570\u4f7f\u7528\u201coutput chr cin\u201d\u6587\u4ef6\u5939\u4e2d\u521b\u5efa\u7684CIN\u5bf9\u8c61\uff0c\u5e76\u5728\u201coutput chr plots\u201d\u6587\u4ef6\u5939\u4e2d\u521b\u5efa\u603b\u517118\u4e2a\u56fe\u50cf\uff0c\u6bcf\u4e2a\u53c2\u6570\u8bbe\u7f6e\u4e00\u4e2a\u56fe\u50cf\uff0c\u663e\u793a\u6bcf\u4e2a\u67d3\u8272\u4f53\u7684\u4e0d\u7a33\u5b9a\u6307\u6570\u3002\u751f\u6210\u7684\u6240\u6709\u56fe\u50cf\u8fd8\u5c06\u6c47\u603b\u5230\u4e00\u4e2apdf\u6587\u4ef6\u4e2d\uff0c\u5982\u4e0b\u56fe\u6240\u793a\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u5728\u4e0a\u56fe\u4e2d\uff0c\u989c\u8272\u6e10\u53d8\u53cd\u6620\u4e86\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u6307\u6570\u7684\u503c\u3002\u4ee5\u7ea2\u8272\u663e\u793a\u6269\u589e\uff0c\u4ee5\u84dd\u8272\u663e\u793a\u635f\u5931\u3002\u603b\u4f53\u4e0d\u7a33\u5b9a\u6027\uff08\u79f0\u4e3a\u201csum\u201d\uff09\u663e\u793a\u4e3a\u9ec4\u8272\uff0c\u8868\u793a\u540c\u65f6\u5b58\u5728\u6269\u589e\u548c\u635f\u5931\u3002\u9ed1\u8272\u8868\u793a\u6ca1\u6709\u4e0d\u7a33\u5b9a\u6027\uff0c\u989c\u8272\u8d8a\u4eae\uff0c\u4e0d\u7a33\u5b9a\u6027\u8d8a\u9ad8\u3002<\/p>\n\n\n\n

\u5206\u6790\u5355\u4e2a\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027<\/strong><\/strong><\/p>\n\n\n\n

\u7ecf\u8fc7\u4ee5\u4e0a\u7684\u5206\u6790\uff0c\u6211\u4eec\u6ce8\u610f\u5230\u6269\u589e\u9608\u503c\u4e3a2.25\uff0c\u635f\u5931\u9608\u503c\u4e3a1.75\uff0c\u5e76\u4e0d\u4f7f\u7528\u5f52\u4e00\u5316\u65f6\uff0c\u5bf9\u5e94\u7684sum\u56fe\u4e2d\u4e0d\u7a33\u5b9a\u548c\u7a33\u5b9a\u7684\u67d3\u8272\u4f53\u5bf9\u6bd4\u8f83\u4e3a\u660e\u663e\uff0c\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528run.cin.cyto()\u51fd\u6570\u5728\u8be5\u53c2\u6570\u8bbe\u7f6e\u6761\u4ef6\u4e0b\u5bf9\u5355\u4e2a\u67d3\u8272\u4f53\u8fdb\u884c\u4e0d\u7a33\u5b9a\u5206\u6790\uff0c\u5e76\u7ed8\u5236\u7ed3\u679c\u70ed\u56fe\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

run.cin.cyto(grl.seg = grl.data, cnvgr=cnvgr.18.auto, snpgr=snpgr.18.auto, genome.ucsc = hg18.ucsctrack,thr.gain = 2.25,thr.loss = 1.75, V.def = 3, V.mode=”sum”) # \u8fd0\u884crun.cin.cyto\u51fd\u6570\u8ba1\u7b97\u7ec6\u80de\u9057\u4f20\u5b66\u5e26\uff08cytoband\uff09\u7ea7\u522b\u7684\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u6307\u6570\uff08CIN\uff09\uff0c\u8f93\u5165\u6570\u636e\u4e3agrl.data\uff08\u62f7\u8d1d\u6570\u53d8\u5f02\u6570\u636e\uff09\uff0ccnvgr.18.auto\uff08CNV\u63a2\u9488\u6ce8\u91ca\uff09\uff0csnpgr.18.auto\uff08SNP\u63a2\u9488\u6ce8\u91ca\uff09\uff0c\u4ee5\u53ca\u53c2\u8003\u57fa\u56e0\u7ec4\u6ce8\u91ca\uff0cthr.gain\u548cthr.loss\u53c2\u6570\u6307\u5b9a\u4e86\u62f7\u8d1d\u6570\u589e\u52a0\u548c\u51cf\u5c11\u7684\u9608\u503c\uff0cV.def\u548cV.mode\u53c2\u6570\u5b9a\u4e49\u4e86\u8ba1\u7b97CIN\u6307\u6570\u7684\u6a21\u5f0f\u548c\u65b9\u6cd5<\/p>\n\n\n\n

comp.heatmap(R_or_C=”Cytobands”, clinical.inf=clin.crc, genome.ucsc=hg18.ucsctrack, in.folder.name=”output_cyto_cin”, out.folder.name=”output_cyto_plots”, thr.gain=2.25, thr.loss=1.75,V.def=3,V.mode=’sum’) # \u751f\u6210\u7ec6\u80de\u9057\u4f20\u5b66\u5e26\u7ea7\u522b\u7684CIN\u6307\u6570\u70ed\u56fe\uff0cR_or_C\u53c2\u6570\u4e3a”Cytobands”\uff0c\u8868\u793a\u4f7f\u7528\u7ec6\u80de\u9057\u4f20\u5b66\u5e26\u7f16\u53f7\uff0c clinical.inf\u53c2\u6570\u4e3a\u4e34\u5e8a\u4fe1\u606f\uff0cgenome.ucsc\u53c2\u6570\u4e3a\u53c2\u8003\u57fa\u56e0\u7ec4\u6ce8\u91ca\uff0cin.folder.name\u548cout.folder.name\u53c2\u6570\u5206\u522b\u6307\u5b9a\u8f93\u5165\u6570\u636e\u548c\u8f93\u51fa\u56fe\u7247\u7684\u6587\u4ef6\u5939\u540d\u79f0\uff0cthr.gain\u548cthr.loss\u53c2\u6570\u7528\u4e8e\u7ed8\u5236\u70ed\u56fe\u65f6\u7684\u9608\u503c\u8bbe\u7f6e\uff0cV.def\u548cV.mode\u53c2\u6570\u4e0e\u8ba1\u7b97CIN\u6307\u6570\u65f6\u7684\u8bbe\u7f6e\u4e00\u81f4<\/p>\n\n\n\n

\u4ee5\u4e0a\u4ee3\u7801\u8fd0\u884c\u65f6\u95f4\u8f83\u957f\uff0c\u9700\u8981\u540c\u5b66\u4eec\u8010\u5fc3\u7b49\u5f85\uff0c\u8fd0\u884c\u7ed3\u675f\u540e\uff0c\u4f1a\u751f\u621022\u4e2a\u67d3\u8272\u4f53\u7684\u4e0d\u7a33\u5b9a\u5206\u6790\u7ed3\u679c\u70ed\u56fe\uff0c\u5176\u4e2d\u6211\u4eec\u4ee520\u53f7\u67d3\u8272\u4f53\u7684\u7ed3\u679c\u4e3a\u4f8b\uff0c\u7ed3\u679c\u4e3a\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u753120\u53f7\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u5206\u6790\u7684\u7ed3\u679c\u70ed\u56fe\u53ef\u77e5\uff0c\u6bcf\u4e00\u884c\u8868\u793a\u4e00\u4e2a\u6837\u672c\uff08s1\u81f3s10\uff09\uff0c\u5176\u4e2ds1\u81f3s5\u4e3a\u590d\u53d1\u6837\u672c\uff0cs6\u81f3s10\u4e3a\u975e\u590d\u53d1\u6837\u672c\u3002X\u8f74\u8868\u793a\u67d3\u8272\u4f5320\u4e0a\u4e0d\u540c\u7684\u7ec6\u80de\u5e26\uff08cytobands\uff09\uff0c\u4ecep13\u5230q13.33\u3002\u989c\u8272\u6e10\u53d8\u53cd\u6620\u4e86\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u6307\u6570\u7684\u503c\uff1a\u9ec4\u8272\u8868\u793a\u4e0d\u7a33\u5b9a\u6027\u9ad8\uff0c\u9ed1\u8272\u8868\u793a\u6ca1\u6709\u4e0d\u7a33\u5b9a\u6027\u3002\u4ece\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fa\uff0c\u975e\u590d\u53d1\u6837\u672c\uff08s6\u81f3s10\uff09\u5728\u591a\u4e2a\u7ec6\u80de\u5e26\u4e0a\u663e\u793a\u51fa\u663e\u8457\u7684\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\uff0c\u7279\u522b\u662f\u5728q13.12\u3001q12.1\u3001q13.2\u7b49\u4f4d\u7f6e\uff0c\u663e\u793a\u51fa\u5927\u9762\u79ef\u7684\u9ec4\u8272\u533a\u57df\uff0c\u8868\u660e\u8fd9\u4e9b\u4f4d\u7f6e\u5b58\u5728\u9ad8\u6c34\u5e73\u7684\u57fa\u56e0\u6269\u589e\u548c\u7f3a\u5931\u3002\u800c\u590d\u53d1\u6837\u672c\uff08s1\u81f3s5\uff09\u5219\u5728\u5927\u591a\u6570\u7ec6\u80de\u5e26\u4e0a\u663e\u793a\u51fa\u76f8\u5bf9\u8f83\u4f4e\u7684\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\uff0c\u4ec5\u5728\u5c11\u6570\u4f4d\u7f6e\u6709\u5c11\u91cf\u7684\u9ec4\u8272\u533a\u57df\u3002\u6574\u4f53\u6765\u770b\uff0c\u590d\u53d1\u6837\u672c\u7684\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u663e\u8457\u4f4e\u4e8e\u975e\u590d\u53d1\u6837\u672c\uff0c\u8fd9\u53ef\u80fd\u4e0e\u590d\u53d1\u6837\u672c\u4e2d\u80bf\u7624\u7ec6\u80de\u7684\u57fa\u56e0\u53d8\u5f02\u6709\u5173\u3002<\/p>\n\n\n\n

\u4ee5\u4e0a\u5c31\u662f\u5bf9CINdex\u5305\u7684\u5168\u90e8\u4ecb\u7ecd\u4e86\u3002CINdex\u5305\u662f\u4e00\u4e2a\u4e13\u4e3a\u57fa\u56e0\u7ec4\u4e0d\u7a33\u5b9a\u6027\u7814\u7a76\u8bbe\u8ba1\u7684\u5de5\u5177\uff0c\u65e8\u5728\u5206\u6790\u548c\u91cf\u5316\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u3002\u901a\u8fc7CINdex\u5305\uff0c\u6211\u4eec\u80fd\u591f\u8ba1\u7b97\u67d3\u8272\u4f53\u4e0d\u7a33\u5b9a\u6027\u6307\u6570\uff0c\u8bc4\u4f30\u6837\u672c\u4e2d\u67d3\u8272\u4f53\u7684\u62f7\u8d1d\u6570\u53d8\u5f02\uff0c\u5e76\u53ef\u89c6\u5316\u8fd9\u4e9b\u53d8\u5f02\u60c5\u51b5\u3002\u5728\u4eca\u5929\u7684\u5b66\u4e60\u4e2d\uff0c\u6211\u4eec\u8be6\u7ec6\u8bb2\u89e3\u4e86CINdex\u5305\u7684\u5b89\u88c5\u6b65\u9aa4\u548c\u4f7f\u7528\u793a\u4f8b\uff0c\u5c55\u793a\u4e86\u5176\u5728\u80bf\u7624\u7814\u7a76\u4e2d\u7684\u5e94\u7528\u6f5c\u529b\u548c\u5206\u6790\u80fd\u529b\u3002\u5e0c\u671b\u540c\u5b66\u4eec\u80fd\u591f\u6df1\u5165\u7406\u89e3\u548c\u719f\u7ec3\u5e94\u7528CINdex\u5305\uff0c\u5171\u540c\u63a8\u52a8\u751f\u7269\u4fe1\u606f\u5b66\u548c\u533b\u5b66\u9886\u57df\u7684\u7814\u7a76\u8fdb\u5c55\uff01<\/p>\n\n\n\n

\u540c\u5b66\u4eec\u5982\u679c\u89c9\u5f97\u81ea\u5df1\u5199\u4ee3\u7801\u9ebb\u70e6\uff0c\u53ef\u4ee5\u4f53\u9a8c\u4e00\u4e0b\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177\uff0c\u53ea\u9700\u8f93\u5165\u6570\u636e\uff0c\u5373\u53ef\u8f7b\u677e\u751f\u6210\u6240\u9700\u56fe\u8868\u3002\u7acb\u5373\u8bbf\u95ee\u4e91\u751f\u4fe1\uff08<\/a><\/strong>http:\/\/www.biocloudservice.com\/home.html<\/u><\/a>\uff09\uff0c\u5f00\u542f\u4fbf\u6377\u7684\u751f\u4fe1\u4e4b\u65c5\uff01<\/strong><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

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