{"id":61237,"date":"2024-10-28T14:28:21","date_gmt":"2024-10-28T06:28:21","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61237"},"modified":"2024-10-28T14:28:21","modified_gmt":"2024-10-28T06:28:21","slug":"wgbs%e6%95%b0%e6%8d%ae%e8%bd%bb%e6%9d%be%e6%90%9e%e5%ae%9a%ef%bc%81bsseq%e5%8c%85%ef%bc%8c%e8%ae%a9%e5%b7%ae%e5%bc%82%e7%94%b2%e5%9f%ba%e5%8c%96%e5%8c%ba%e5%9f%9f%e6%97%a0%e5%a4%84%e9%81%81%e5%bd%a2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61237","title":{"rendered":"WGBS\u6570\u636e\u8f7b\u677e\u641e\u5b9a\uff01bsseq\u5305\uff0c\u8ba9\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\u65e0\u5904\u9041\u5f62\uff01"},"content":{"rendered":"\n

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

\u79d1\u7814\u5c0f\u4f19\u4f34\u4eec\uff0c\u9762\u5bf9\u5806\u79ef\u5982\u5c71\u7684WGBS\u6570\u636e\uff0c\u662f\u5426\u611f\u5230\u65e0\u4ece\u4e0b\u624b\uff1f\u522b\u62c5\u5fc3\uff0c\u6709\u4e86bsseq\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u9a7e\u9a6dBSmooth\u7b97\u6cd5\uff0c\u8ba9\u590d\u6742\u7684\u6570\u636e\u5206\u6790\u53d8\u5f97\u7b80\u5355\u3002<\/p>\n\n\n\n

\u5168\u57fa\u56e0\u7ec4\u7532\u57fa\u5316\u6d4b\u5e8f\uff08Whole Genome Bisulfite Sequencing, WGBS\uff09\u662f\u4e00\u79cd\u7528\u4e8e\u68c0\u6d4bDNA\u7532\u57fa\u5316\u72b6\u6001\u7684\u9ad8\u901a\u91cf\u6d4b\u5e8f\u6280\u672f\u3002DNA\u7532\u57fa\u5316\u662f\u4e00\u79cd\u91cd\u8981\u7684\u8868\u89c2\u9057\u4f20\u4fee\u9970\uff0c\u5b83\u5728\u8c03\u63a7\u57fa\u56e0\u8868\u8fbe\u3001\u80da\u80ce\u53d1\u80b2\u3001\u7ec6\u80de\u5206\u5316\u4ee5\u53ca\u8bb8\u591a\u75be\u75c5\u7684\u53d1\u751f\u53d1\u5c55\u4e2d\u626e\u6f14\u7740\u5173\u952e\u89d2\u8272\u3002\u901a\u8fc7WGBS\u6280\u672f\uff0c\u7814\u7a76\u4eba\u5458\u53ef\u4ee5\u5728\u6574\u4e2a\u57fa\u56e0\u7ec4\u8303\u56f4\u5185\u7cbe\u786e\u5730\u5b9a\u4f4d\u7532\u57fa\u5316\u4f4d\u70b9\uff0c\u6d4b\u91cf\u7279\u5b9a\u57fa\u56e0\u7ec4\u533a\u57df\u7684\u7532\u57fa\u5316\u6c34\u5e73\uff0c\u8fd9\u5bf9\u4e8e\u7406\u89e3\u57fa\u56e0\u8868\u8fbe\u8c03\u63a7\u3001\u75be\u75c5\u53d1\u5c55\u4e43\u81f3\u751f\u7269\u8fdb\u5316\u90fd\u81f3\u5173\u91cd\u8981\u3002<\/p>\n\n\n\n

\u800cbsseq\u5305\u5c31\u662f\u4e00\u4e2a\u4e13\u95e8\u7528\u4e8eWGBS\u6570\u636e\u5206\u6790\u7684\u5de5\u5177\uff0c\u5b83\u80fd\u5e2e\u52a9\u6211\u4eec\u4ece\u6d77\u91cf\u6570\u636e\u4e2d\u7cbe\u51c6\u8bc6\u522b\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff08DMRs\uff09\u3002\u8be5\u7b97\u6cd5\u81eaHansen\u7b49\u4eba\u7684\u7814\u7a76\u4e2d\u9996\u6b21\u4eae\u76f8\u4ee5\u6765\uff0c\u5df2\u7ecf\u6210\u4e3a\u6211\u4eec\u5206\u6790WGBS\u6570\u636e\u7684\u5f97\u529b\u52a9\u624b\u3002<\/p>\n\n\n\n

\u4eca\u5929\uff0c\u5c0f\u5e08\u59b9\u5c06\u5e26\u9886\u5927\u5bb6\u4ece\u57fa\u7840\u7684\u6570\u636e\u51c6\u5907\u5f00\u59cb\uff0c\u9010\u6b65\u6df1\u5165\u5230\u9ad8\u7ea7\u5206\u6790\u6280\u5de7\uff0c\u65e0\u8bba\u4f60\u662f\u751f\u7269\u4fe1\u606f\u5b66\u7684\u65b0\u624b\u8fd8\u662f\u8d44\u6df1\u7814\u7a76\u8005\uff0cbsseq\u5305\u90fd\u5c06\u662f\u4f60\u7684\u5f97\u529b\u52a9\u624b\u3002\u6ce8\u610f\u54e6\uff0c\u8fd9\u4e2a<\/strong>R\u5305\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668<\/strong>\u54e6<\/strong>\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u5e08\u59b9\u79df\u8d41\u6027\u4ef7\u6bd4\u9ad8\u7684\u670d\u52a1\u5668<\/strong>~<\/strong><\/p>\n\n\n\n

\u51c6\u5907\u597d\u4e86\u5417\uff1f\u8ba9\u6211\u4eec\u643a\u624b\u8e0f\u4e0a\u8fd9\u573a\u57fa\u56e0\u7ec4\u7532\u57fa\u5316\u5206\u6790\u7684\u5947\u5999\u4e4b\u65c5\uff0c\u4e00\u8d77\u63a2\u7d22\u57fa\u56e0\u7ec4\u7684\u5965\u79d8\uff0c\u63ed\u5f00\u751f\u547d\u79d1\u5b66\u4e2d\u90a3\u4e9b\u9690\u85cf\u7684\u79d8\u5bc6\u3002\u65c5\u9014\u4e2d\u9047\u5230\u4efb\u4f55\u96be\u9898\uff0c\u8bb0\u5f97\u627e\u5c0f\u5e08\u59b9\u54e6\uff0c\u6211\u968f\u65f6\u51c6\u5907\u7740\u5e2e\u4f60\u7b54\u7591\u89e3\u60d1\uff01<\/strong><\/p>\n\n\n\n

\u4e00\u3001<\/strong> <\/strong>\u52a0\u8f7d<\/strong>\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\uff0c\u8ba9\u6211\u4eec\u5f00\u59cb\u5b89\u88c5bsseq\u5305\u548c\u53e6\u5916\u9700\u8981\u7528\u5230\u7684\u5305\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(“bsseq”)<\/p>\n\n\n\n

\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u9700\u8981\u52a0\u8f7d`bsseq`\u548c`bsseqData`\u5e93\uff0c\u7136\u540e\u52a0\u8f7d\u5e76\u66f4\u65b0`BS.cancer.ex`\u6570\u636e\u96c6\uff0c\u5b83\u5305\u542b\u4e86\u672a\u7ecf\u5e73\u6ed1\u5904\u7406\u7684\u201c\u539f\u59cb\u201d\u6c47\u603b\u6bd4\u5bf9\u6570\u636e\u3002<\/p>\n\n\n\n

library(bsseq)<\/p>\n\n\n\n

library(bsseqData)<\/p>\n\n\n\n

# \u52a0\u8f7dBS.cancer.ex\u6570\u636e\u96c6<\/p>\n\n\n\n

data(BS.cancer.ex)<\/p>\n\n\n\n

# BS.cancer.ex <- updateObject(BS.cancer.ex)<\/p>\n\n\n\n

BS.cancer.ex<\/p>\n\n\n\n

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

`BS.cancer.ex`\u5bf9\u8c61\u5305\u542b\u4e86958,541\u4e2a\u7532\u57fa\u5316\u4f4d\u70b9\u548c6\u4e2a\u6837\u672c\uff0c\u8fd9\u4e9b\u6570\u636e\u5c1a\u672a\u8fdb\u884c\u5e73\u6ed1\u5904\u7406\uff0c\u6240\u6709\u5206\u6790\u90fd\u5728\u5185\u5b58\u4e2d\u8fdb\u884c\u3002\u901a\u8fc7\u67e5\u770b`pData(BS.cancer.ex)`\uff0c\u6211\u4eec\u53ef\u4ee5\u4e86\u89e3\u5230\u8fd9\u4e9b\u6837\u672c\u7684\u7c7b\u578b\u548c\u914d\u5bf9\u4fe1\u606f\u3002\u6bcf\u4e2a\u6837\u672c\u90fd\u88ab\u6807\u8bb0\u4e3a\u764c\u75c7\uff08cancer\uff09\u6216\u6b63\u5e38\uff08normal\uff09\uff0c\u5e76\u5206\u914d\u4e86\u4e00\u4e2a\u914d\u5bf9\u7f16\u53f7\uff08pair1, pair2, pair3\uff09\u3002<\/p>\n\n\n\n

# \u67e5\u770b\u6837\u672c\u6570\u636e\u6846\u67b6<\/p>\n\n\n\n

pData(BS.cancer.ex)<\/p>\n\n\n\n

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

\u8f93\u51fa\u663e\u793a\u4e86\u4e00\u4e2a\u5305\u542b6\u884c2\u5217\u7684\u6570\u636e\u6846\u67b6\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u6837\u672c\u7c7b\u578b\u548c\u914d\u5bf9\u4fe1\u606f\u3002\u4f8b\u5982\uff0cC1\u3001C2\u548cC3\u4ee3\u8868\u764c\u75c7\u6837\u672c\uff0c\u800cN1\u3001N2\u548cN3\u4ee3\u8868\u6b63\u5e38\u6837\u672c\uff0c\u5b83\u4eec\u5206\u522b\u4e0epair1\u3001pair2\u548cpair3\u914d\u5bf9\u3002<\/p>\n\n\n\n

\u4e8c\u3001<\/strong> \u6570\u636e\u5e73\u6ed1\u5904\u7406<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u5206\u6790\u7684\u7b2c\u4e00\u6b65\u4e2d\uff0c\u6211\u4eec\u9700\u8981\u5bf9\u6570\u636e\u8fdb\u884c\u5e73\u6ed1\u5904\u7406\u4ee5\u51cf\u5c11\u566a\u58f0\u5e76\u63d0\u9ad8\u6570\u636e\u7684\u53ef\u8bfb\u6027\u3002<\/p>\n\n\n\n

BS.cancer.ex.fit <- BSmooth(<\/p>\n\n\n\n

    BSseq = BS.cancer.ex,<\/p>\n\n\n\n

    BPPARAM = MulticoreParam(workers = 1),<\/p>\n\n\n\n

    verbose = TRUE)<\/p>\n\n\n\n

\u5728\u8fd9\u91cc\uff0c\u6211\u4eec\u5148\u4e0d\u6267\u884c\u8fd9\u6bb5\u4ee3\u7801\u54e6~ \u5982\u679c\u4f60\u7684\u8ba1\u7b97\u673a\u67096\u4e2a\u6838\u5fc3\u53ef\u7528\uff0c\u53ef\u4ee5\u5c06`mc.cores`\u8bbe\u7f6e\u4e3a6\uff0c\u4f46\u662fWindows\u7cfb\u7edf\u4e0a\u4e0d\u652f\u6301\u5c06`mc.cores`\u8bbe\u7f6e\u4e3a\u5927\u4e8e1\u7684\u503c\u3002<\/p>\n\n\n\n

\u4e3a\u4e86\u65b9\u4fbf\u4f7f\u7528\uff0c`bsseqData`\u5df2\u7ecf\u5305\u542b\u4e86\u8fd9\u4e2a\u547d\u4ee4\u7684\u7ed3\u679c\uff1a<\/p>\n\n\n\n

data(BS.cancer.ex.fit)<\/p>\n\n\n\n

BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit)<\/p>\n\n\n\n

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

\u8f93\u51fa\u663e\u793a\u4e86\u4e00\u4e2a`BSseq`\u7c7b\u578b\u7684\u5bf9\u8c61\uff0c\u5305\u542b\u4e86958,541\u4e2a\u7532\u57fa\u5316\u4f4d\u70b9\u548c6\u4e2a\u6837\u672c\uff0c\u5df2\u7ecf\u4f7f\u7528BSmooth\u7b97\u6cd5\u8fdb\u884c\u4e86\u5e73\u6ed1\u5904\u7406\u3002<\/p>\n\n\n\n

\u5e76\u884c\u5316\u5904\u7406<\/strong><\/strong><\/p>\n\n\n\n

\u8fd9\u4e2a\u6b65\u9aa4\u4f7f\u7528\u4e86\u5e76\u884c\u5316\u5904\u7406\uff0c\u6bcf\u4e2a\u6837\u672c\u90fd\u5728\u5355\u72ec\u7684\u6838\u5fc3\u4e0a\u8fd0\u884c\uff0c\u4f7f\u7528\u4e86`parallel`\u5305\u4e2d\u7684`mclapply()`\u51fd\u6570\u3002\u8fd9\u79cd\u5e76\u884c\u5316\u5904\u7406\u5185\u7f6e\u4e8e`bsseq`\u4e2d\uff0c\u9700\u8981\u4e00\u53f0\u62e5\u67096\u4e2a\u6838\u5fc3\u548c\u8db3\u591fRAM\u7684\u8ba1\u7b97\u673a\u3002\u5e73\u6ed1\u6b65\u9aa4\u5728\u6bcf\u4e2a\u6837\u672c\u4e0a\u5b8c\u5168\u72ec\u7acb\u8fdb\u884c\uff0c\u56e0\u6b64\u5982\u679c\u6709\u5f88\u591a\u6837\u672c\uff08\u6216\u5176\u4ed6\u60c5\u51b5\uff09\uff0c\u4e5f\u53ef\u4ee5\u624b\u52a8\u5206\u5272\u8ba1\u7b97\u3002<\/p>\n\n\n\n

CpG\u4f4d\u70b9\u7684\u8986\u76d6\u5ea6<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u5168\u57fa\u56e0\u7ec4\u7532\u57fa\u5316\u6d4b\u5e8f\u4e2d\uff0cCpG\u4f4d\u70b9\u7684\u8986\u76d6\u5ea6\u662f\u4e00\u4e2a\u5173\u952e\u6307\u6807\u3002<\/strong><\/p>\n\n\n\n

`BS.cancer.ex`\u5bf9\u8c61\u5305\u542b\u4e86\u4eba\u7c7b21\u53f7\u548c22\u53f7\u67d3\u8272\u4f53\u4e0a\u6240\u6709\u6ce8\u91ca\u7684CpG\u4f4d\u70b9\u3002\u56e0\u4e3a\u6211\u4eec\u6709\u591a\u4e2a\u6837\u672c\uff0c\u6211\u4eec\u53ef\u4ee5\u5c06\u57fa\u56e0\u7ec4\u5927\u81f4\u5206\u4e3a\u4e09\u7c7b\uff1a\u6240\u6709\u6837\u672c\u90fd\u6709\u6570\u636e\u7684CpG\u4f4d\u70b9\u3001\u6240\u6709\u6837\u672c\u90fd\u6ca1\u6709\u6570\u636e\u7684CpG\u4f4d\u70b9\uff0c\u4ee5\u53ca\u90e8\u5206\u6837\u672c\u6709\u6570\u636e\u7684CpG\u4f4d\u70b9\u3002\u68c0\u67e5\u5f53\u524d\u5bf9\u8c61\uff0c\u6211\u4eec\u53ef\u4ee5\u5f97\u5230\uff1a<\/p>\n\n\n\n

# \u4e24\u4e2a\u67d3\u8272\u4f53\u4e0aCpG\u4f4d\u70b9\u7684\u5e73\u5747\u8986\u76d6\u5ea6<\/p>\n\n\n\n

round(colMeans(getCoverage(BS.cancer.ex)), 1)<\/p>\n\n\n\n

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

# CpG\u4f4d\u70b9\u7684\u6570\u91cf<\/p>\n\n\n\n

length(BS.cancer.ex)<\/p>\n\n\n\n

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

# \u6240\u67096\u4e2a\u6837\u672c\u4e2d\u81f3\u5c11\u88ab1\u4e2a\u8bfb\u53d6\u8986\u76d6\u7684CpG\u4f4d\u70b9\u6570\u91cf<\/p>\n\n\n\n

sum(rowSums(getCoverage(BS.cancer.ex) >= 1) == 6)<\/p>\n\n\n\n

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

# \u6240\u6709\u6837\u672c\u4e2d\u8986\u76d6\u5ea6\u4e3a0\u7684CpG\u4f4d\u70b9\u6570\u91cf<\/p>\n\n\n\n

sum(rowSums(getCoverage(BS.cancer.ex)) == 0)<\/p>\n\n\n\n

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

\u7531\u6b64\u6211\u4eec\u53ef\u4ee5\u77e5\u9053\u8986\u76d6\u5ea6\u5927\u81f4\u4e3a4\u500d\uff0c\u56e0\u6b64\u6211\u4eec\u9884\u671f\u4f1a\u6709\u5f88\u591a\u8986\u76d6\u5ea6\u4e3a0\u7684CpG\u4f4d\u70b9\u3002\u4f46\u662f\uff0c\u4e0d\u662f\u8bf4\u6bcf\u4e2aCpG\u4f4d\u70b9\u5728\u6240\u67096\u4e2a\u6837\u672c\u91cc\u90fd\u4f1a\u8986\u76d6\u5ea6\u4e3a\u96f6\uff0c\u8fd9\u4e8b\u513f\u6ca1\u90a3\u4e48\u7edd\u5bf9\u3002<\/p>\n\n\n\n

\u4e3a\u4e86\u66f4\u597d\u5730\u7406\u89e3\u8fd9\u4e00\u70b9\uff0c\u6211\u4eec\u53ef\u4ee5\u5047\u8bbe\u5168\u57fa\u56e0\u7ec4\u7684\u8986\u76d6\u5ea6\u9075\u5faa\u53c2\u6570\u4e3a4\u7684\u6cca\u677e\u5206\u5e03\u3002\u5728\u8fd9\u79cd\u60c5\u51b5\u4e0b\uff0c\u6211\u4eec\u53ef\u4ee5\u8ba1\u7b97\u81f3\u5c11\u6709\u4e00\u4e2a\u6837\u672c\u8986\u76d6\u5ea6\u4e3a\u96f6\u7684CpG\u4f4d\u70b9\u7684\u9884\u671f\u6bd4\u4f8b\u3002<\/p>\n\n\n\n

# \u8ba1\u7b97\u6cca\u677e\u5206\u5e03\u7684\u6982\u7387<\/p>\n\n\n\n

logp <- ppois(0, lambda = 4, lower.tail = FALSE, log.p = TRUE)# \u8ba1\u7b97\u81f3\u5c11\u6709\u4e00\u4e2a\u6837\u672c\u8986\u76d6\u5ea6\u4e3a\u96f6\u7684CpG\u4f4d\u70b9\u7684\u6bd4\u4f8b<\/p>\n\n\n\n

round(1 – exp(6 * logp), 3)<\/p>\n\n\n\n

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

\u8fd9\u6bb5\u4ee3\u7801\u7684\u8f93\u51fa\u7ed3\u679c\u8868\u660e\uff0c\u6211\u4eec\u9884\u671f\u5927\u7ea6\u670910.5%\u7684CpG\u4f4d\u70b9\u81f3\u5c11\u5728\u4e00\u4e2a\u6837\u672c\u4e2d\u7684\u8986\u76d6\u5ea6\u4e3a\u96f6\u3002\u8fd9\u4e2a\u8ba1\u7b97\u6709\u52a9\u4e8e\u6211\u4eec\u7406\u89e3\u6570\u636e\u4e2d\u7684\u96f6\u8986\u76d6\u73b0\u8c61\uff0c\u5e76\u5728\u540e\u7eed\u5206\u6790\u4e2d\u5bf9\u8fd9\u4e9bCpG\u4f4d\u70b9\u8fdb\u884c\u9002\u5f53\u7684\u5904\u7406\u3002<\/p>\n\n\n\n

\u6211\u4eec\u7684\u6570\u636e\u91cc\uff0c\u6709\u597d\u4e9bCpG\u4f4d\u70b9\u5728\u516d\u4e2a\u6837\u672c\u91cc\u90fd\u6ca1\u5565\u4fe1\u606f\uff0c\u5dee\u4e0d\u591a\u670913\u4e07\u4e2a\u5427\u3002\u8fd9\u53ef\u80fd\u662f\u56e0\u4e3a\u8fd9\u4e9b\u4f4d\u70b9\u592a\u50b2\u5a07\u4e86\uff0c\u4e0d\u5bb9\u6613\u88ab\u6620\u5c04\u5230\u57fa\u56e0\u7ec4\u4e0a\u3002\u6211\u4eec\u73b0\u5728\u7528\u7684\u8fd8\u662f50bp\u7684\u5355\u7aef\u6d4b\u5e8f\uff0c\u8981\u662f\u6362\u6210100bp\u7684\u914d\u5bf9\u672b\u7aef\u6d4b\u5e8f\uff0c\u80fd\u6620\u5c04\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u4f1a\u591a\u4e0d\u5c11\u5462\u3002\u5bf9\u4e8e\u90a3\u4e9b\u5728\u6240\u6709\u6837\u672c\u4e2d\u8986\u76d6\u5ea6\u90fd\u4e3a\u96f6\u7684CpG\u4f4d\u70b9\uff0c\u6211\u4eec\u5904\u7406\u8d77\u6765\u8fd8\u7b97\u7b80\u5355\uff0c\u4f46\u5f97\u51fa\u7ed3\u8bba\u65f6\u5f97\u60a0\u7740\u70b9\u3002<\/p>\n\n\n\n

\u8fd8\u6709\u554a\uff0c\u6709\u4e9bCpG\u4f4d\u70b9\u5728\u90e8\u5206\u6837\u672c\u4e2d\u9ed8\u9ed8\u65e0\u95fb\uff0c\u5728\u90e8\u5206\u6837\u672c\u4e2d\u8986\u76d6\u5ea6\u4e3a\u96f6\uff0c\u4f46\u4e0d\u662f\u5168\u90e8\u3002\u8fd9\u4e9b\u4f4d\u70b9\u5c31\u68d8\u624b\u4e86\uff0c\u56e0\u4e3a\u6211\u4eec\u7684\u8986\u76d6\u5ea6\u672c\u6765\u5c31\u4e0d\u9ad8\uff0c\u5076\u5c14\u4e00\u4e2a\u6837\u672c\u6ca1\u8986\u76d6\u5230\u4e5f\u662f\u6b63\u5e38\u7684\uff0c\u8981\u662f\u76f4\u63a5\u6392\u9664\u8fd9\u4e9b\u4f4d\u70b9\uff0c\u53ef\u80fd\u5c31\u592a\u6b66\u65ad\u4e86\u3002<\/p>\n\n\n\n

\u5e73\u6ed1\u5904\u7406\u7684\u6280\u5de7<\/strong><\/p>\n\n\n\n

\u63a5\u4e0b\u6765\u8bf4\u8bf4\u5e73\u6ed1\u5904\u7406\u3002\u6211\u4eec\u5f97\u5bf9\u6bcf\u4e2a\u6837\u672c\u5355\u72ec\u505a\u5e73\u6ed1\uff0c\u53ea\u7528\u90a3\u4e9b\u8986\u76d6\u5ea6\u975e\u96f6\u7684\u4f4d\u70b9\u3002\u8fd9\u6837\u5c31\u80fd\u4f30\u8ba1\u51fa\u5168\u57fa\u56e0\u7ec4\u7684\u7532\u57fa\u5316\u60c5\u51b5\uff0c\u7136\u540e\u7ed9BSseq\u5bf9\u8c61\u91cc\u7684\u6bcf\u4e2aCpG\u4f4d\u70b9\u90fd\u4f30\u4e2a\u7532\u57fa\u5316\u503c\u3002\u8fd9\u62db\u5728\u6bd4\u8f83\u4e0d\u540c\u6837\u672c\u7684\u540c\u4e00\u4e2aCpG\u4f4d\u70b9\u65f6\u7279\u7ed9\u529b\uff0c\u5c24\u5176\u662f\u90a3\u4e9b\u5076\u5c14\u8986\u76d6\u5ea6\u4e3a\u96f6\u7684\u6837\u672c\u3002\u4e0d\u8fc7\uff0c\u5982\u679c\u57fa\u56e0\u7ec4\u67d0\u4e9b\u533a\u57df\u9644\u8fd1\u538b\u6839\u5c31\u6ca1\u8986\u76d6\u5230CpG\u4f4d\u70b9\uff0c\u90a3\u5e73\u6ed1\u540e\u7684\u7532\u57fa\u5316\u8f6e\u5ed3\u5c31\u6ca1\u591a\u5927\u610f\u4e49\u4e86\u3002\u6211\u4eec\u53ef\u4ee5\u5728\u5e73\u6ed1\u540e\u628a\u8fd9\u4e9b\u4f4d\u70b9\u5254\u9664\u6389\u3002<\/p>\n\n\n\n

\u624b\u52a8\u5206\u5272\u5e73\u6ed1\u8ba1\u7b97<\/strong><\/strong><\/p>\n\n\n\n

\u4ee5\u4e0b\u662f\u4e00\u4e2a\u624b\u52a8\u5206\u5272\u5e73\u6ed1\u8ba1\u7b97\u793a\u4f8b\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u5148\u53ea\u4f7f\u7528\u6837\u672c1\u548c2\uff1a<\/p>\n\n\n\n

# \u5206\u5272\u6570\u636e<\/p>\n\n\n\n

BS1 <- BS.cancer.ex[, 1]<\/p>\n\n\n\n

save(BS1, file = “BS1.rda”)<\/p>\n\n\n\n

BS2 <- BS.cancer.ex[, 2]<\/p>\n\n\n\n

save(BS1, file = “BS1.rda”)<\/p>\n\n\n\n

# \u5728\u6bcf\u4e2a\u8282\u70b9\u4e0a\u6267\u884c\u4ee5\u4e0b\u64cd\u4f5c<\/p>\n\n\n\n

# \u8282\u70b91<\/p>\n\n\n\n

load(“BS1.rda”)<\/p>\n\n\n\n

BS1.fit <- BSmooth(BS1)<\/p>\n\n\n\n

save(BS1.fit)<\/p>\n\n\n\n

save(BS1.fit, file = “BS1.fit.rda”)<\/p>\n\n\n\n

# \u8282\u70b92<\/p>\n\n\n\n

load(“BS2.rda”)<\/p>\n\n\n\n

BS2.fit <- BSmooth(BS2)<\/p>\n\n\n\n

save(BS2.fit, file = “BS2.fit.rda”)<\/p>\n\n\n\n

# \u5408\u5e76\uff08\u5728\u65b0\u7684R\u4f1a\u8bdd\u4e2d\uff09<\/p>\n\n\n\n

load(“BS1.fit.rda”)<\/p>\n\n\n\n

load(“BS2.fit.rda”)<\/p>\n\n\n\n

BS.fit <- combine(BS1.fit, BS2.fit)<\/p>\n\n\n\n

\u6ce8\u610f\u54e6\uff0c\u8fd9\u4ecd\u9700\u8981\u6709\u4e00\u4e2a\u8282\u70b9\u6709\u8db3\u591f\u7684RAM\u6765\u5bb9\u7eb3\u6240\u6709\u6837\u672c\u3002<\/p>\n\n\n\n

\u4e09\u3001<\/strong>\u8ba1\u7b97t\u7edf\u8ba1\u91cf<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u8ba1\u7b97t\u7edf\u8ba1\u91cf\u4e4b\u524d\uff0c\u6211\u4eec\u5f97\u5148\u6e05\u7406\u4e00\u4e0b\u6570\u636e\u3002\u90a3\u4e9b\u8986\u76d6\u5ea6\u5f88\u4f4e\u6216\u8005\u6839\u672c\u6ca1\u6709\u8986\u76d6\u7684CpG\u4f4d\u70b9\uff0c\u6211\u4eec\u5c31\u4e0d\u8981\u4e86\u3002\u8981\u662f\u4e0d\u8fd9\u4e48\u505a\uff0c\u4f60\u53ef\u80fd\u4f1a\u5728\u8986\u76d6\u5ea6\u5f88\u4f4e\u7684\u57fa\u56e0\u7ec4\u533a\u57df\u627e\u5230\u5f88\u591a\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff08DMRs\uff09\uff0c\u8fd9\u4e9b\u5f88\u53ef\u80fd\u662f\u5047\u9633\u6027\u3002\u5177\u4f53\u8981\u53bb\u6389\u54ea\u4e9bCpG\u4f4d\u70b9\uff0c\u8fd9\u5f97\u770b\u4e2a\u4eba\u559c\u597d\uff0c\u4f46\u5728\u8fd9\u4e2a\u5206\u6790\u4e2d\uff0c\u6211\u4eec\u53ea\u4fdd\u7559\u81f3\u5c11\u6709\u4e24\u4e2a\u764c\u75c7\u6837\u672c\u548c\u81f3\u5c11\u6709\u4e24\u4e2a\u6b63\u5e38\u6837\u672c\u8986\u76d6\u5ea6\u81f3\u5c11\u4e3a2\u500d\u7684CpG\u4f4d\u70b9\u3002\u4e3a\u4e86\u770b\u8d77\u6765\u66f4\u6e05\u695a\uff0c\u6211\u4eec\u628a\u8986\u76d6\u5ea6\u6570\u636e\u5b58\u5728\u4e00\u4e2a\u5355\u72ec\u7684\u77e9\u9635\u91cc\u3002<\/p>\n\n\n\n

BS.cov <- getCoverage(BS.cancer.ex.fit)<\/p>\n\n\n\n

keepLoci.ex <- which(rowSums(BS.cov[, BS.cancer.ex$Type == “cancer”] >= 2) >= 2 &<\/p>\n\n\n\n

                     rowSums(BS.cov[, BS.cancer.ex$Type == “normal”] >= 2) >= 2)<\/p>\n\n\n\n

length(keepLoci.ex)<\/p>\n\n\n\n

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

BS.cancer.ex.fit <- BS.cancer.ex.fit[keepLoci.ex,]<\/p>\n\n\n\n

\u73b0\u5728\uff0c\u6211\u4eec\u5df2\u7ecf\u53ef\u4ee5\u5f00\u59cb\u8ba1\u7b97t\u7edf\u8ba1\u91cf\u4e86\u3002<\/p>\n\n\n\n

BS.cancer.ex.tstat <- BSmooth.tstat(BS.cancer.ex.fit,<\/p>\n\n\n\n

                                    group1 = c(“C1”, “C2”, “C3”),<\/p>\n\n\n\n

                                    group2 = c(“N1”, “N2”, “N3”),<\/p>\n\n\n\n

                                    estimate.var = “group2”,<\/p>\n\n\n\n

                                    local.correct = TRUE,<\/p>\n\n\n\n

                                    verbose = TRUE)<\/p>\n\n\n\n

BS.cancer.ex.tstat<\/p>\n\n\n\n

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

 t\u7edf\u8ba1\u91cf\u7684\u8ba1\u7b97\u8fc7\u7a0b<\/strong><\/strong><\/p>\n\n\n\n

`BSmooth.tstat()`\u51fd\u6570\u7684\u53c2\u6570\u633a\u7b80\u5355\u7684\u3002`group1`\u548c`group2`\u5305\u542b\u4e86\u4e24\u7ec4\u88ab\u6bd4\u8f83\u7684\u6837\u672c\u540d\u79f0\uff08\u603b\u662f`group1`\u51cf\u53bb`group2`\uff09\uff0c\u4e5f\u53ef\u4ee5\u7528\u7d22\u5f15\u4ee3\u66ff\u6837\u672c\u540d\u79f0\u3002`estimate.var`\u53c2\u6570\u63cf\u8ff0\u4e86\u7528\u54ea\u4e9b\u6837\u672c\u6765\u4f30\u8ba1\u53d8\u5f02\u6027\u3002\u56e0\u4e3a\u8fd9\u4e2a\u662f\u764c\u75c7\u6570\u636e\u96c6\uff0c\u764c\u75c7\u6837\u672c\u7684\u53d8\u5f02\u6027\u6bd4\u6b63\u5e38\u6837\u672c\u9ad8\uff0c\u6240\u4ee5\u6211\u4eec\u53ea\u7528\u6b63\u5e38\u6837\u672c\u6765\u4f30\u8ba1\u53d8\u5f02\u6027\u3002`estimate.var`\u7684\u5176\u4ed6\u9009\u62e9\u6709`same`\uff08\u5047\u8bbe\u6bcf\u7ec4\u7684\u53d8\u5f02\u6027\u76f8\u540c\uff09\u548c`paired`\uff08\u505a\u4e00\u4e2a\u914d\u5bf9t\u68c0\u9a8c\uff09\u3002`local.correct`\u53c2\u6570\u63cf\u8ff0\u4e86\u6211\u4eec\u662f\u5426\u5e94\u8be5\u4f7f\u7528\u5927\u89c4\u6a21\uff08\u4f4e\u9891\uff09\u5747\u503c\u6821\u6b63\u3002\u8fd9\u5728\u764c\u75c7\u7814\u7a76\u4e2d\u5c24\u5176\u91cd\u8981\uff0c\u56e0\u4e3a\u6211\u4eec\u53d1\u73b0\u764c\u75c7\u548c\u6b63\u5e38\u7ec4\u7ec7\u4e4b\u95f4\u5b58\u5728\u5f88\u591a\u5927\u89c4\u6a21\u7684\u7532\u57fa\u5316\u5dee\u5f02\u3002<\/p>\n\n\n\n

\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u4ee5\u4e0b\u4ee3\u7801\u67e5\u770bt\u7edf\u8ba1\u91cf\u7684\u8fb9\u9645\u5206\u5e03\uff1a<\/p>\n\n\n\n

plot(BS.cancer.ex.tstat)<\/p>\n\n\n\n

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

\u5728\u672a\u6821\u6b63\u7684t\u7edf\u8ba1\u91cf\u7684\u8fb9\u9645\u5206\u5e03\u4e2d\uff0c\u53ef\u4ee5\u6e05\u695a\u5730\u770b\u5230\u4f4e\u7532\u57fa\u5316\u201c\u5757\u201d\u3002<\/p>\n\n\n\n

\u5373\u4f7f\u5728\u6ca1\u6709\u89c2\u5bdf\u5230\u8fd9\u4e9b\u5927\u89c4\u6a21\u7532\u57fa\u5316\u5dee\u5f02\u7684\u6bd4\u8f83\u4e2d\uff0c\u5bf9t\u7edf\u8ba1\u91cf\u8fdb\u884c\u5c40\u90e8\u6821\u6b63\u901a\u5e38\u4e5f\u4f1a\u6539\u5584\u5b83\u4eec\u7684\u8fb9\u9645\u5206\u5e03\uff08\u201c\u6539\u5584\u201d\u662f\u6307\u4f7f\u5b83\u4eec\u66f4\u52a0\u5bf9\u79f0\uff09\u3002<\/p>\n\n\n\n

\u6821\u6b63t\u7edf\u8ba1\u91cf\u7684\u610f\u4e49<\/strong><\/p>\n\n\n\n

\u5c40\u90e8\u6821\u6b63t\u7edf\u8ba1\u91cf\u7684\u610f\u4e49\u5728\u4e8e\uff0c\u5b83\u80fd\u5e2e\u52a9\u6211\u4eec\u5f97\u5230\u66f4\u52a0\u51c6\u786e\u7684\u7532\u57fa\u5316\u5dee\u5f02\u533a\u57df\u3002\u901a\u8fc7\u8fd9\u79cd\u65b9\u6cd5\uff0c\u6211\u4eec\u53ef\u4ee5\u51cf\u5c11\u7531\u4e8e\u5076\u7136\u56e0\u7d20\u6216\u5b9e\u9a8c\u8bef\u5dee\u5bfc\u81f4\u7684\u5047\u9633\u6027\u7ed3\u679c\uff0c\u4ece\u800c\u66f4\u6709\u4fe1\u5fc3\u5730\u6307\u51fa\u771f\u6b63\u7684\u751f\u7269\u5b66\u5dee\u5f02\u3002\u8fd9\u79cd\u6821\u6b63\u65b9\u6cd5\u5728\u5904\u7406\u5927\u89c4\u6a21\u7532\u57fa\u5316\u6570\u636e\u65f6\u5c24\u4e3a\u91cd\u8981\uff0c\u56e0\u4e3a\u5b83\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u8bc6\u522b\u51fa\u90a3\u4e9b\u5728\u764c\u75c7\u548c\u6b63\u5e38\u7ec4\u7ec7\u4e4b\u95f4\u5b58\u5728\u663e\u8457\u5dee\u5f02\u7684\u533a\u57df\u3002<\/p>\n\n\n\n

\u56db\u3001<\/strong>\u5bfb\u627e\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff08DMRs\uff09<\/strong><\/p>\n\n\n\n

\u563f\u563f\uff0c\u8bf4\u5230\u8fd9\u513f\uff0c\u5c0f\u5e08\u59b9\u5f97\u63d0\u4e00\u4e0b\uff0c\u7b49\u6211\u4eec\u628at\u7edf\u8ba1\u91cf\u4e00\u7b97\u51fa\u6765\uff0c\u5c31\u80fd\u5212\u62c9\u4e2a\u6807\u51c6\u7ebf\uff0c\u4e5f\u5c31\u662f\u9608\u503c\uff0c\u6765\u6311\u51fa\u90a3\u4e9b\u7532\u57fa\u5316\u7a0b\u5ea6\u4e0d\u4e00\u6837\u7684\u5730\u65b9\uff0c\u4e13\u4e1a\u70b9\u8bf4\u5c31\u662f\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff0c\u7b80\u79f0DMRs\u3002\u6211\u4eec\u8fd9\u6b21\u5212\u7684\u7ebf\u662f4.6\uff0c\u8fd9\u4e2a\u6570\u5b57\u53ef\u4e0d\u662f\u62cd\u8111\u888b\u5b9a\u7684\uff0c\u662f\u597d\u597d\u7785\u4e86\u7785\u6574\u4e2a\u57fa\u56e0\u7ec4\u7684t\u7edf\u8ba1\u91cf\u7684\u5206\u5e03\u60c5\u51b5\uff0c\u6311\u4e86\u4e2a\u5408\u9002\u7684\u5206\u4f4d\u6570\u503c\u3002\u8fd9\u6837\u4e00\u6765\uff0c\u6211\u4eec\u5c31\u80fd\u628a\u90a3\u4e9b\u7532\u57fa\u5316\u7a0b\u5ea6\u53d8\u5316\u5927\u7684\u533a\u57df\u7ed9\u6807\u8bb0\u51fa\u6765\u4e86\u3002<\/p>\n\n\n\n

\u662f\u4e0d\u662f\u633a\u6709\u610f\u601d\u7684\uff1f\u6211\u4eec\u5c31\u8fd9\u4e48\u4e00\u6b65\u6b65\u5730\uff0c\u628a\u57fa\u56e0\u7ec4\u7684\u79d8\u5bc6\u7ed9\u63ed\u5f00\u5566\uff01<\/p>\n\n\n\n

dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6))<\/p>\n\n\n\n

## [dmrFinder] creating dmr data.frame<\/p>\n\n\n\n

dmrs <- subset(dmrs0, n >= 3 & abs(meanDiff) >= 0.1)<\/p>\n\n\n\n

nrow(dmrs)<\/p>\n\n\n\n

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

\u8fd9\u6bb5\u4ee3\u7801\u7684\u8f93\u51fa\u544a\u8bc9\u6211\u4eec\uff0c\u6211\u4eec\u627e\u5230\u4e86373\u4e2aDMRs\u3002\u6211\u4eec\u8fdb\u4e00\u6b65\u7b5b\u9009\u51fa\u90a3\u4e9b\u81f3\u5c11\u5305\u542b3\u4e2aCpG\u4f4d\u70b9\uff0c\u5e76\u4e14\u5728\u6b63\u5e38\u548c\u764c\u75c7\u6837\u672c\u4e4b\u95f4\u7684\u7532\u57fa\u5316\u5e73\u5747\u5dee\u5f02\u81f3\u5c11\u4e3a0.1\u7684DMRs\u3002<\/p>\n\n\n\n

head(dmrs, n = 3)<\/p>\n\n\n\n

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

\u63a5\u4e0b\u6765\uff0c\u5c0f\u5e08\u59b9\u6765\u7ed9\u4f60\u4eec\u8bf4\u8bf4\u6211\u4eec\u600e\u4e48\u6311\u51fa\u90a3\u4e9b\u7279\u522b\u6709\u610f\u601d\u7684DMRs\u3002\u6211\u4eec\u5148\u770b\u8f93\u51fa\uff0c\u5b83\u4f1a\u544a\u8bc9\u6211\u4eec\u524d\u4e09\u4e2aDMRs\u7684\u8be6\u7ec6\u4fe1\u606f\uff0c\u6bd4\u5982\u5b83\u4eec\u5728\u57fa\u56e0\u7ec4\u7684\u54ea\u4e2a\u4f4d\u7f6e\uff0c\u7275\u6d89\u5230\u591a\u5c11\u4e2aCpG\u4f4d\u70b9\uff0c\u533a\u57df\u6709\u591a\u5927\uff0c\u8fd8\u6709\u5404\u79cd\u7edf\u8ba1\u6570\u636e\uff0c\u6bd4\u5982\u5e73\u5747\u5dee\u5f02\u3001\u4e24\u7ec4\u6837\u672c\u7684\u5e73\u5747\u7532\u57fa\u5316\u6c34\u5e73\u4e4b\u7c7b\u7684\u3002\u8fd9\u4e9b\u6570\u636e\u53ef\u5e2e\u6211\u4eec\u5927\u5fd9\u4e86\uff0c\u80fd\u8ba9\u6211\u4eec\u6e05\u695a\u5730\u770b\u5230\u54ea\u4e9b\u533a\u57df\u5728\u6b63\u5e38\u548c\u764c\u75c7\u6837\u672c\u4e4b\u95f4\u7684\u7532\u57fa\u5316\u7a0b\u5ea6\u53d8\u5316\u6700\u5927\u3002<\/p>\n\n\n\n

\u6311DMRs\u7684\u65f6\u5019\uff0c\u6211\u4eec\u5f97\u5b9a\u4e2a\u89c4\u77e9\uff0c\u6bd4\u5982\u8bf4\uff0c\u6211\u4eec\u5c31\u4e0d\u8981\u90a3\u4e9bCpG\u4f4d\u70b9\u5c11\u4e8e3\u4e2a\uff0c\u6216\u8005\u7532\u57fa\u5316\u5dee\u5f02\u592a\u5c0f\uff08\u5c0f\u4e8e0.1\uff09\u7684\u533a\u57df\u3002\u867d\u7136\u8fd9\u4e2a\u89c4\u77e9\u7684\u5177\u4f53\u6570\u5b57\u53ef\u4ee5\u5546\u91cf\uff0c\u4f46\u6709\u4e2a\u6807\u51c6\u603b\u662f\u597d\u7684\u3002<\/p>\n\n\n\n

`dmrFinder()`\u51fd\u6570\u8fd8\u6709\u4e2a\u633a\u9177\u7684\u529f\u80fd\uff0c\u5c31\u662f\u53ef\u4ee5\u8bbe\u7f6e`qcutoff`\u53c2\u6570\uff0c\u7528\u5206\u4f4d\u6570\u6765\u5b9a\u9608\u503c\u3002\u6bd4\u5982\uff0c\u6211\u4eec\u53ef\u4ee5\u8bbe`qcutoff = c(0.01, 0.99)`\uff0c\u8fd9\u6837\u5c31\u80fd\u6311\u51fa\u90a3\u4e9b\u7532\u57fa\u5316\u5dee\u5f02\u7279\u522b\u5927\u7684\u533a\u57df\u3002\u8fd8\u6709\u4e2a`maxGap`\u53c2\u6570\uff0c\u5982\u679c\u4e24\u4e2aCpG\u4f4d\u70b9\u4e4b\u95f4\u7684\u8ddd\u79bb\u8d85\u8fc7\u4e86\u8fd9\u4e2a\u503c\uff0c\u90a3\u5b83\u4eec\u5c31\u4e0d\u4f1a\u88ab\u7b97\u4f5c\u4e00\u4e2aDMR\u3002<\/p>\n\n\n\n

\u8bf4\u5230\u6392\u5e8f\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e`areaStat`\u8fd9\u4e2a\u6307\u6807\u6765\uff0c\u5b83\u5176\u5b9e\u5c31\u662f\u6bcf\u4e2aCpG\u4f4d\u70b9\u7684t\u7edf\u8ba1\u91cf\u52a0\u5728\u4e00\u8d77\u3002\u8fd9\u4e2a\u6307\u6807\u6709\u70b9\u50cf\u662fDMR\u7684\u201c\u9762\u79ef\u201d\uff0c\u4f46\u5b83\u662f\u6839\u636eCpG\u4f4d\u70b9\u7684\u6570\u91cf\u6765\u52a0\u6743\u7684\uff0c\u800c\u4e0d\u662f\u770b\u5b83\u4eec\u5728\u57fa\u56e0\u7ec4\u91cc\u5360\u591a\u957f\u3002\u867d\u7136\u8fd9\u4e2a\u65b9\u6cd5\u5df2\u7ecf\u4e0d\u9519\u4e86\uff0c\u4f46\u6211\u4eec\u8fd8\u662f\u5e0c\u671b\u80fd\u6709\u66f4\u597d\u7684\u529e\u6cd5\u3002<\/p>\n\n\n\n

\u603b\u4e4b\u5462\uff0c\u7528\u8fd9\u4e9b\u65b9\u6cd5\uff0c\u6211\u4eec\u5c31\u80fd\u66f4\u7cbe\u786e\u5730\u627e\u5230\u90a3\u4e9b\u5728\u764c\u75c7\u548c\u6b63\u5e38\u7ec4\u7ec7\u4e4b\u95f4\u7532\u57fa\u5316\u6c34\u5e73\u6709\u660e\u663e\u5dee\u5f02\u7684\u533a\u57df\uff0c\u8fd9\u5bf9\u4e8e\u641e\u751f\u7269\u7814\u7a76\u6216\u8005\u60f3\u641e\u70b9\u4e34\u5e8a\u5e94\u7528\u7684\u5e08\u5144\u5e08\u59d0\u4eec\u6765\u8bf4\uff0c\u53ef\u662f\u8d85\u7ea7\u6709\u7528\u7684\u4fe1\u606f\u54e6\uff01<\/p>\n\n\n\n

\u4e94\u3001<\/strong>\u7ed8\u5236DMRs\u56fe<\/strong><\/p>\n\n\n\n

\u8bf4\u5230\u67e5\u770b\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff0c\u4e5f\u5c31\u662fDMRs\uff0c\u8fd9\u53ef\u662f\u54b1\u4eec\u7814\u7a76\u4e2d\u7684\u91cd\u8981\u4e00\u6b65\u5462\u3002\u4e3a\u4e86\u8ba9\u8fd9\u4e9b\u533a\u57df\u5728\u56fe\u4e0a\u66f4\u663e\u773c\uff0c\u54b1\u4eec\u53ef\u4ee5\u5728pData\u91cc\u52a0\u4e0a\u4e00\u4e9b\u7279\u522b\u7684\u6807\u8bb0\uff0c\u6bd4\u5982\u989c\u8272\u3001\u7ebf\u578b\u548c\u7ebf\u5bbd\u3002<\/p>\n\n\n\n

\u5c31\u50cf\u8fd9\u6837\uff0c\u54b1\u4eec\u5148\u8bbe\u7f6e\u597dpData\uff1a<\/p>\n\n\n\n

pData <- pData(BS.cancer.ex.fit)<\/p>\n\n\n\n

pData$col <- rep(c(“red”, “blue”), each = 3)<\/p>\n\n\n\n

pData(BS.cancer.ex.fit) <- pData<\/p>\n\n\n\n

\u7136\u540e\uff0c\u54b1\u4eec\u5c31\u53ef\u4ee5\u5f00\u59cb\u753b\u56fe\u5566\uff0c\u6bd4\u5982\u753b\u7b2c\u4e00\u4e2aDMR\uff1a<\/p>\n\n\n\n

plotRegion(BS.cancer.ex.fit, dmrs[1,], extend = 5000, addRegions = dmrs)<\/p>\n\n\n\n

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

\u8fd9\u91cc\u7684extend\u5c31\u662f\u8bf4\uff0c\u54b1\u4eec\u8981\u5728\u56fe\u7684\u4e24\u8fb9\u5404\u6269\u5c55\u591a\u5c11\u78b1\u57fa\u5bf9\u3002\u800caddRegions\u5c31\u662f\u544a\u8bc9\u54b1\u4eec\uff0c\u8fd8\u6709\u54ea\u4e9b\u533a\u57df\u9700\u8981\u7279\u522b\u6807\u6ce8\u4e00\u4e0b\u3002<\/p>\n\n\n\n

\u5f53\u7136\u4e86\uff0c\u54b1\u4eec\u901a\u5e38\u4e0d\u4f1a\u53ea\u753b\u4e00\u4e2aDMR\uff0c\u800c\u662f\u4f1a\u4e00\u6b21\u6027\u753b\u4e0a\u597d\u51e0\u767e\u4e2a\uff0c\u7136\u540e\u5b58\u5230\u4e00\u4e2aPDF\u6587\u4ef6\u91cc\uff0c\u7528\u522b\u7684\u5de5\u5177\u6162\u6162\u770b\u3002\u8fd9\u65f6\u5019\uff0cplotManyRegions()\u51fd\u6570\u5c31\u6d3e\u4e0a\u7528\u573a\u4e86\uff0c\u5b83\u6bd4\u4e00\u4e2a\u4e00\u4e2a\u5730\u7528plotRegion()\u753b\u8981\u5feb\u5f97\u591a\u3002\u4e3e\u4e2a\u4f8b\u5b50\uff1a<\/p>\n\n\n\n

pdf(file = “dmrs_top200.pdf”, width = 10, height = 5)<\/p>\n\n\n\n

plotManyRegions(BS.cancer.ex.fit, dmrs[1:200,], extend = 5000,<\/p>\n\n\n\n

                addRegions = dmrs)<\/p>\n\n\n\n

dev.off()<\/p>\n\n\n\n

\u8fd9\u6bb5\u4ee3\u7801\u5c31\u4f1a\u5e2e\u54b1\u4eec\u628a\u524d200\u4e2aDMRs\u90fd\u753b\u51fa\u6765\uff0c\u4fdd\u5b58\u5728pdf\u4e2d\u5566\uff0c\u8fd9\u6837\u80fd\u8ba9\u6211\u4eec\u5728\u540e\u7eed\u7684\u5206\u6790\u6216\u62a5\u544a\u4e2d\u5feb\u901f\u56de\u987e\u548c\u5c55\u793a\u6211\u4eec\u7684\u53d1\u73b0\u3002\u8fd9\u79cd\u53ef\u89c6\u5316\u7684\u65b9\u6cd5\uff0c\u5728\u5411\u522b\u4eba\u89e3\u91ca\u590d\u6742\u7684\u7532\u57fa\u5316\u6570\u636e\u65f6\uff0c\u7279\u522b\u6709\u7528\u54e6\u3002<\/p>\n\n\n\n

\u597d\u5566\uff0c\u54b1\u4eec\u4eca\u5929\u7684\u7532\u57fa\u5316\u6570\u636e\u5206\u6790\u5c0f\u8bfe\u5802\u5c31\u5230\u8fd9\u91cc\u4e86\u3002\u5c0f\u5e08\u59b9\u5e26\u7740\u5927\u5bb6\u4e00\u8d77\u4ece\u6570\u636e\u7684\u9884\u5904\u7406\uff0c\u5230\u5e73\u6ed1\u5904\u7406\uff0c\u518d\u5230\u627e\u51fa\u5dee\u5f02\u7532\u57fa\u5316\u533a\u57df\uff08DMRs\uff09\uff0c\u6700\u540e\u8fd8\u4e00\u8d77\u770b\u4e86\u600e\u4e48\u628a\u8fd9\u4e9b\u533a\u57df\u753b\u51fa\u6765\u3002\u5e0c\u671b\u4f60\u4eec\u90fd\u80fd\u8ddf\u4e0a\u8282\u594f\uff0c\u5bf9\u8fd9\u4e9b\u590d\u6742\u7684\u6570\u636e\u5206\u6790\u6709\u4e86\u66f4\u6df1\u7684\u7406\u89e3\u3002<\/p>\n\n\n\n

\u8bb0\u5f97\u54e6\uff0c\u6570\u636e\u5206\u6790\u5c31\u50cf\u662f\u89e3\u8c1c\u6e38\u620f\uff0c\u6bcf\u4e00\u6b65\u90fd\u5f88\u91cd\u8981\u3002\u54b1\u4eec\u7528\u5230\u7684\u8fd9\u4e9b\u5de5\u5177\u548c\u65b9\u6cd5\uff0c\u5c31\u50cf\u662f\u89e3\u8c1c\u65f6\u7684\u5c0f\u9053\u5177\uff0c\u7528\u5f97\u597d\u4e86\uff0c\u5c31\u80fd\u5e2e\u54b1\u4eec\u66f4\u5feb\u5730\u627e\u5230\u7b54\u6848\u3002\u6240\u4ee5\uff0c\u5927\u5bb6\u5728\u5b9e\u9645\u64cd\u4f5c\u7684\u65f6\u5019\uff0c\u4e00\u5b9a\u8981\u7ec6\u5fc3\uff0c\u591a\u5c1d\u8bd5\uff0c\u591a\u601d\u8003\u3002<\/p>\n\n\n\n

\u5982\u679c\u4f60\u4eec\u5728\u5206\u6790\u7684\u8fc7\u7a0b\u4e2d\u9047\u5230\u4ec0\u4e48\u96be\u9898\uff0c\u6216\u8005\u6709\u4ec0\u4e48\u65b0\u53d1\u73b0\uff0c\u968f\u65f6\u6b22\u8fce\u6765\u627e\u5c0f\u5e08\u59b9\u8ba8\u8bba\u54e6\u3002<\/strong>\u6211\u4eec\u4e00\u8d77\u5b66\u4e60\uff0c\u4e00\u8d77\u8fdb\u6b65\u3002\u6bd5\u7adf\uff0c\u79d1\u5b66\u7684\u9053\u8def\u4e0a\uff0c\u6211\u4eec\u4ece\u4e0d\u5b64\u5355\uff01<\/p>\n\n\n\n

\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\u6b22\u8fce\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u795e\u5668\uff0c\u53ea\u9700\u4e00\u952e\u4e0a\u4f20\u6570\u636e\uff0c\u60f3\u8981\u7684\u56fe\u5c31\u80fd\u8f7b\u677eget~<\/strong><\/strong><\/p>\n\n\n\n

\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/strong>http:\/\/www.biocloudservice.com\/home.html<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

\u79d1\u7814\u5c0f\u4f19\u4f34\u4eec\uff0c\u9762\u5bf9\u5806\u79ef\u5982\u5c71\u7684WGBS\u6570\u636e\uff0c\u662f\u5426\u611f\u5230\u65e0\u4ece\u4e0b\u624b\uff1f\u522b\u62c5\u5fc3\uff0c\u6709\u4e86bsseq\u5305\uff0c\u6211\u4eec\u53ef\u4ee5\u8f7b\u677e\u9a7e\u9a6dBSmo […]<\/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\/61237"}],"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=61237"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61237\/revisions"}],"predecessor-version":[{"id":61252,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61237\/revisions\/61252"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61237"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61237"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61237"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}