{"id":26280,"date":"2024-01-25T12:18:08","date_gmt":"2024-01-25T04:18:08","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26280"},"modified":"2024-01-25T12:18:10","modified_gmt":"2024-01-25T04:18:10","slug":"%e5%ad%a6%e4%bc%9acmplot%ef%bc%8c%e7%bb%98%e5%88%b6%e5%87%ba%e6%af%94qqman%e6%9b%b4%e4%bc%98%e7%a7%80%e7%9a%84gwas%e5%8f%af%e8%a7%86%e5%8c%96%e7%bb%93%e6%9e%9c","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26280","title":{"rendered":"\u5b66\u4f1aCMplot\uff0c\u7ed8\u5236\u51fa\u6bd4qqman\u66f4\u4f18\u79c0\u7684GWAS\u53ef\u89c6\u5316\u7ed3\u679c"},"content":{"rendered":"

\u5728\u6700\u8fd1\u7684\u8fd9\u6bb5\u65f6\u95f4\u91cc\u76f8\u4fe1\u505a\u79d1\u7814\u7684\u5404\u4f4d\u5c0f\u4f19\u4f34\u90fd\u88abGWAS\u548c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5237\u8fc7\u5c4f\uff0c\u5c0f\u679c\u4e5f\u6709\u5728\u505a\u6559\u5b66\u7684\u63a8\u6587\u54e6~\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5173\u6ce8\u6211\u4eec\u7684\u516c\u4f17\u53f7\u751f\u4fe1\u679c\u8fdb\u884c\u4e86\u89e3\u5b66\u4e60\u5440\uff01<\/p>\n

<\/a>\u80cc\u666f\u77e5\u8bc6<\/h1>\n

\u73b0\u5728\uff0c\u8ba9\u5c0f\u679c\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u4e3a\u4f55GWAS\u548c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5177\u6709\u5982\u6b64\u7d27\u5bc6\u7684\u8054\u7cfb\u5427\uff01<\/p>\n

\u5b5f\u5fb7\u5c14\u968f\u673a\u5316(Mendelian Randomization)\u8fd1\u6765\u5907\u53d7\u6b22\u8fce\uff0c\u5176\u4e2d\u90e8\u5206\u539f\u56e0\u5728\u4e8e\u5b83\u80fd\u591f\u6700\u5927\u7a0b\u5ea6\u5730\u51cf\u5c11\u5176\u4ed6\u89c2\u5bdf\u6027\u6d41\u884c\u75c5\u5b66\u7814\u7a76\u8bbe\u8ba1\u4e2d\u7684\u4e24\u4e2a\u4e3b\u8981\u95ee\u9898\uff1a\u6df7\u6742\u56e0\u7d20\u548c\u9006\u5411\u56e0\u679c\u3002\u901a\u8fc7\u5c06\u9057\u4f20\u53d8\u5f02\u89c6\u4e3a\u4e00\u79cd\u201c\u81ea\u7136\u7684\u968f\u673a\u5316\u5b9e\u9a8c\u201d\uff0cMendelian Randomization\u80fd\u591f\u63d0\u4f9b\u5173\u4e8e\u53ef\u8c03\u63a7\u98ce\u9669\u56e0\u7d20\u4e0e\u75be\u75c5\u4e4b\u95f4\u53ef\u80fd\u7684\u56e0\u679c\u5173\u7cfb\u7684\u8bc1\u636e\u3002\u6b64\u5916\uff0c\u76f8\u8f83\u4e8e\u968f\u673a\u4e34\u5e8a\u8bd5\u9a8c\uff0cMendelian Randomization\u6240\u9700\u7684\u65f6\u95f4\u548c\u6210\u672c\u8f83\u5c11\uff0c\u540c\u65f6\u80fd\u591f\u5206\u6790\u73b0\u6709\u7814\u7a76\u5e76\u89e3\u51b3\u968f\u673a\u4e34\u5e8a\u8bd5\u9a8c\u65e0\u6cd5\u89e3\u51b3\u7684\u95ee\u9898\u3002<\/p>\n

\u4e0e\u6b64\u540c\u65f6\uff0c\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u7814\u7a76(GWAS)\u4e5f\u53d8\u5f97\u8d8a\u6765\u8d8a\u53d7\u6b22\u8fce\uff0c\u56e0\u4e3a\u5b83\u53ef\u4ee5\u53d1\u73b0\u5728Mendelian Randomization\u7814\u7a76\u4e2d\u8c03\u67e5\u7684\u4e2d\u95f4\u8868\u578b\u4e2d\u5bf9\u53d8\u5f02\u6709\u8d21\u732e\u7684\u591a\u4e2a\u9057\u4f20\u53d8\u5f02\uff0c\u4ece\u800c\u589e\u5f3a\u4e86Mendelian Randomization\u7814\u7a76\u7684\u6548\u529b\u3002<\/p>\n

\u56e0\u6b64\uff0cGWAS\u548c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u4e24\u8005\u7684\u7ed3\u5408\u6210\u4e3a\u4e86\u5f53\u524d\u7814\u7a76\u9886\u57df\u7684\u65b0\u70ed\u70b9\u4e4b\u4e00\u3002<\/p>\n

<\/h1>\n

\u800c\u5c0f\u679c\u4eca\u5929\u60f3\u5206\u4eab\u7ed9\u5927\u5bb6\u7684R\u5305CMplot\u662f\u4e00\u6b3e\u4e13\u95e8\u7ed8\u5236GWAS\u4e2d\u975e\u5e38\u91cd\u8981\u7684\u53ef\u89c6\u5316\u5de5\u5177\u2013\u66fc\u54c8\u987f\u56fe\u7684R\u5305\uff0c\u4e0e\u5c0f\u679c\u4e4b\u524d\u4ecb\u7ecd\u8fc7\u7684qqman\u4e0d\u540c\uff0cCMplot\u5305\u53ea\u6709\u4e00\u4e2a\u51fd\u6570\uff0c\u4f46\u901a\u8fc7\u53c2\u6570\u7684\u8bbe\u7f6e\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u901a\u8fc7\u8fd9\u4e00\u4e2a\u51fd\u6570\u7ed8\u5236\u51faSNP\u5bc6\u5ea6\u56fe\uff0c\u666e\u901a\/\u73af\u72b6\u7684\u66fc\u54c8\u987f\u56fe\uff0c\u4ee5\u53caQQ\u56fe\u3002<\/p>\n

\u4ee5\u4e0b\u662f\u66fc\u54c8\u987f\u56fe\u5728GWAS\u4e2d\u7684\u91cd\u8981\u6027\uff1a<\/p>\n

\u63d0\u4f9b\u6240\u6709\u5173\u8054\u7684\u6982\u89c8\uff1a\u66fc\u54c8\u987f\u56fe\u7b80\u6d01\u5730\u603b\u7ed3\u4e86\u6574\u4e2a\u57fa\u56e0\u7ec4\u4e2d\u57fa\u56e0\u578b(SNP\u3001indels\u7b49)\u4e0e\u8868\u578b\u4e4b\u95f4\u7684\u5173\u8054\u7ed3\u679c\u3002\u8fd9\u4f7f\u5f97\u6240\u6709\u5173\u8054\u53ef\u4ee5\u4e00\u76ee\u4e86\u7136\u5730\u67e5\u770b\u3002 \u786e\u5b9a\u663e\u8457\u533a\u57df\uff1ay\u8f74\u663e\u793a\u5173\u8054\u7684\u5f3a\u5ea6\uff0c\u4f7f\u7528-log10 p\u503c\u3002\u7a81\u7834\u663e\u8457\u6027\u9608\u503c\u7684\u5cf0\u503c\u5bb9\u6613\u8bc6\u522b\u4e3a\u6f5c\u5728\u7684\u8868\u578b\u98ce\u9669\u4f4d\u70b9\u3002 \u663e\u793a\u7a7a\u95f4\u6a21\u5f0f\uff1a\u53ef\u4ee5\u89c2\u5bdf\u6cbfx\u8f74\u6392\u5217\u7684\u67d3\u8272\u4f53\u4e0a\u663e\u8457SNP\u7684\u7a7a\u95f4\u6a21\u5f0f\uff0c\u5982\u805a\u7c7b\u3002\u8fd9\u6709\u52a9\u4e8e\u8bc6\u522b\u5019\u9009\u57fa\u56e0\u3002 \u65b9\u4fbf\u6bd4\u8f83\uff1a\u66fc\u54c8\u987f\u56fe\u5141\u8bb8\u5728\u4e0d\u540c\u7684GWAS\u7ed3\u679c\u4e4b\u95f4\u8fdb\u884c\u89c6\u89c9\u6bd4\u8f83\uff0c\u5982\u75c5\u4f8b\u4e0e\u5bf9\u7167\u7ec4\u4e4b\u95f4\u3002\u5173\u8054\u6a21\u5f0f\u7684\u76f8\u4f3c\u6027\u548c\u5dee\u5f02\u6027\u4e00\u76ee\u4e86\u7136\u3002 \u76f4\u89c2\u89e3\u91ca\uff1a\u66fc\u54c8\u987f\u56fe\u901a\u8fc7\u5bf9\u5f3a\u5173\u8054\u548c\u5f31\u5173\u8054\u7684\u53ef\u89c6\u5316\u5206\u79bb\uff0c\u4f7f\u5176\u80fd\u591f\u5728\u6ca1\u6709\u7edf\u8ba1\u4e13\u4e1a\u77e5\u8bc6\u7684\u60c5\u51b5\u4e0b\u76f4\u89c2\u89e3\u91ca\u3002 \u6709\u52a9\u4e8e\u4f20\u64ad\uff1a\u4f5c\u4e3a\u7b80\u6d01\u7684\u6c47\u603b\u56fe\uff0c\u66fc\u54c8\u987f\u56fe\u5bf9\u4e8e\u5411\u79d1\u5b66\u754c\u548c\u4e00\u822c\u89c2\u4f17\u4f20\u8fbeGWAS\u7684\u5173\u952e\u53d1\u73b0\u975e\u5e38\u6709\u7528\u3002<\/p>\n

\u7ed3\u679c\u7b80\u5355\u7684\u4ecb\u7ecd\u8fc7\u540e\uff0c\u5c31\u7531\u5c0f\u679c\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u6765\u5165\u95e8CMplot\u8fd9\u6b3eR\u5305\u5427\uff01<\/p>\n

# Step 0 \u4e0b\u8f7dR\u5305
\n## CMplot\u53ef\u4ee5\u901a\u8fc7\u6700\u57fa\u672c\u7684\u4e0b\u8f7d\u65b9\u5f0f\u8fdb\u884c\u4e0b\u8f7d\u54e6
\n# install.packages(“CMplot”)
\nlibrary(CMplot)<\/p>\n

# Step 1 \u52a0\u8f7d\u6570\u636e
\n## \u5728CMplot\u4e2d\uff0cR\u5305\u7684\u4f5c\u8005\u4e3a\u6211\u4eec\u51c6\u5907\u4e86\u4e24\u7ec4\u6570\u636e\uff0c\u5206\u522b\u662fcattle50k\u548cpig60k\uff0c\u5c0f\u679c\u4eca\u5929\u4f7f\u7528cattle50k\u4e3a\u5927\u5bb6\u8fdb\u884c\u6f14\u793a
\ndata(“cattle50K”)
\n## \u6211\u4eec\u53ef\u4ee5\u89c2\u5bdf\u4e00\u4e0b\u6570\u636e
\nhead(cattle50K)<\/p>\n

## SNP chr pos Somatic cell score Milk yield Fat percentage
\n## 1 SNP1 1 59082 0.000244361 0.000484255 0.001379210
\n## 2 SNP2 1 118164 0.000532272 0.000039800 0.000598951
\n## 3 SNP3 1 177246 0.001633058 0.000311645 0.000279427
\n## 4 SNP4 1 236328 0.001412865 0.000909370 0.001040161
\n## 5 SNP5 1 295410 0.000090700 0.002202973 0.000351394
\n## 6 SNP6 1 354493 0.000110681 0.000342628 0.000105792<\/p>\n

## \u6570\u636e\u6700\u5c11\u67094\u5217\uff0c\u5206\u522b\u662fSNP\uff0c\u67d3\u8272\u4f53\uff0c\u67d3\u8272\u4f53\u4f4d\u7f6e\u548c\u6027\u72b6\uff0cp.s. \u5728\u8fd9\u7ec4\u6570\u636e\u4e2d\u4e3a\u6211\u4eec\u5c55\u793a\u4e86\u4e09\u4e2a\u6027\u72b6<\/p>\n

\u52a0\u8f7d\u6570\u636e\u8fc7\u540e\u5c31\u8981\u5f00\u59cb\u5b66\u4e60\u4eca\u5929CMplot\u7684\u7ed8\u5236\u5b66\u4e60\u5566\uff01 \u5c0f\u679c\u4e3a\u5927\u5bb6\u505a\u4e86\u4e00\u4e2a\u6240\u6709\u53c2\u6570\u7684\u6c47\u603b\uff0c\u53c2\u6570\u6709\u70b9\u591a\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u5927\u6982\u7684\u6d4f\u89c8\u4e00\u4e0b\u5c31\u53ef\u4ee5\u54e6~<\/p>\n

@ \u57fa\u7840\u53c2\u6570
\nPmap\uff1a\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u81f3\u5c11\u5305\u542b\u56db\u5217\u3002\u7b2c\u4e00\u5217\u662fSNP\u7684\u540d\u79f0\uff0c\u7b2c\u4e8c\u5217\u662fSNP\u7684\u67d3\u8272\u4f53\uff0c\u7b2c\u4e09\u5217\u662fSNP\u7684\u4f4d\u7f6e\uff0c\u5269\u4f59\u7684\u5217\u662f\u6bcf\u4e2a\u7279\u5f81\u7684P\u503c\uff08\u6bcf\u4e2a\u7279\u5f81\u4e00\u4e2a\u5217\uff09\u3002
\nband\uff1a\u67d3\u8272\u4f53\u4e4b\u95f4\u7684\u8ddd\u79bb\uff0c\u9ed8\u8ba4\u4e3a1\uff08\u5982\u679cband\u7b49\u4e8e0\uff0c\u5219\u67d3\u8272\u4f53\u4e4b\u95f4\u5c06\u6ca1\u6709\u95f4\u9694\uff09\u3002
\nH\uff1a\u6bcf\u4e2a\u5706\u7684\u9ad8\u5ea6\uff0c\u6bcf\u4e2a\u5706\u4ee3\u8868\u4e00\u4e2a\u7279\u5f81\uff0c\u9ed8\u8ba4\u4e3a1\u3002
\nplot.type\uff1a\u4e00\u4e2a\u5b57\u7b26\u6216\u5411\u91cf\uff0c\u53ea\u80fd\u4f7f\u7528”d”\u3001”c”\u3001”m”\u3001”q”\u6216”b”\u3002\u5982\u679cplot.type=”d”\uff0c\u5c06\u7ed8\u5236SNP\u5bc6\u5ea6\u56fe\uff1b\u5982\u679cplot.type=”c”\uff0c\u53ea\u7ed8\u5236\u5706\u5f62\u66fc\u54c8\u987f\u56fe\uff1b\u5982\u679cplot.type=”m”\uff0c\u53ea\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\uff1b\u5982\u679cplot.type=”q”\uff0c\u53ea\u7ed8\u5236Q-Q\u56fe\uff1b\u5982\u679cplot.type=”b”\uff0c\u5c06\u7ed8\u5236\u5706\u5f62\u66fc\u54c8\u987f\u56fe\u3001\u66fc\u54c8\u987f\u56fe\u548cQ-Q\u56fe\uff1b\u5982\u679cplot.type=c(“m”,”q”)\uff0c\u5c06\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\u548cQ-Q\u56fe\u3002
\nmultracks\uff1a\u4e00\u4e2a\u903b\u8f91\u503c\uff0c\u5982\u679cmultracks=FALSE\uff0c\u5219\u6240\u6709\u66fc\u54c8\u987f\u56fe\u5c06\u5728\u5206\u79bb\u7684\u6587\u4ef6\u4e2d\u7ed8\u5236\uff0c\u5982\u679c\u4e3aTRUE\uff0c\u5219\u6240\u6709\u66fc\u54c8\u987f\u56fe\u5c06\u7ed8\u5236\u5728\u4e00\u4e2a\u6587\u4ef6\u4e2d\u3002
\npoints.alpha\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u7528\u4e8e\u591a\u7279\u5f81\u66fc\u54c8\u987f\u56fe\u4e2d\u70b9\u7684\u900f\u660e\u5ea6\uff0c\u8303\u56f4\u4ece0\uff08\u5b8c\u5168\u900f\u660e\uff09\u5230255\uff08\u4e0d\u900f\u660e\uff09\u3002
\ncex\uff1a\u4e00\u4e2a\u6570\u5b57\u6216\u5411\u91cf\uff0c\u7528\u4e8e\u70b9\u7684\u5927\u5c0f\uff0c\u4e0e<plot>\u4e2d\u7684”size”\u53c2\u6570\u76f8\u540c\u3002\u5982\u679c\u662f\u5411\u91cf\uff0c\u5219\u7b2c\u4e00\u4e2a\u6570\u5b57\u63a7\u5236\u5706\u5f62\u56fe\u4e2d\u70b9\u7684\u5927\u5c0f\uff08\u9ed8\u8ba4\u4e3a0.5\uff09\uff0c\u7b2c\u4e8c\u4e2a\u6570\u5b57\u63a7\u5236\u66fc\u54c8\u987f\u56fe\u4e2d\u70b9\u7684\u5927\u5c0f\uff08\u9ed8\u8ba4\u4e3a1\uff09\uff0c\u7b2c\u4e09\u4e2a\u6570\u5b57\u63a7\u5236Q-Q\u56fe\u4e2d\u70b9\u7684\u5927\u5c0f\uff08\u9ed8\u8ba4\u4e3a1\uff09\u3002
\nr\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u8868\u793a\u5706\u7684\u534a\u5f84\uff08\u5185\u534a\u5f84\uff09\uff0c\u9ed8\u8ba4\u4e3a1\u3002
\ncol\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u77e9\u9635\u3002\u5982\u679c”col”\u662f\u5411\u91cf\uff0c\u5219\u6bcf\u4e2a\u5706\u4f7f\u7528\u76f8\u540c\u7684\u989c\u8272\uff0c\u8868\u793a\u76f8\u540c\u67d3\u8272\u4f53\u4f7f\u7528\u76f8\u540c\u989c\u8272\u3002\u989c\u8272\u4e0d\u662f\u56fa\u5b9a\u7684\uff0c\u53ef\u4ee5\u4f7f\u7528\u4e00\u4e2a\u3001\u4e24\u4e2a\u3001\u4e09\u4e2a\u6216\u66f4\u591a\u989c\u8272\u3002\u5982\u679c”col”\u7684\u957f\u5ea6\u6bd4\u67d3\u8272\u4f53\u7684\u957f\u5ea6\u77ed\uff0c\u5219\u989c\u8272\u4f1a\u5faa\u73af\u4f7f\u7528\u3002\u5982\u679c”col”\u662f\u77e9\u9635\uff0c\u5219\u884c\u6570\u662f\u7279\u5f81\u7684\u6570\u91cf\uff0c\u5217\u6570\u662f\u7528\u6237\u60f3\u8981\u4e3a\u4e0d\u540c\u7279\u5f81\u4f7f\u7528\u7684\u989c\u8272\u6570\uff0c\u6bcf\u4e2a\u7279\u5f81\u53ef\u4ee5\u7528\u4e0d\u540c\u6570\u91cf\u7684\u989c\u8272\u7ed8\u5236\uff0c\u7f3a\u5931\u503c\u53ef\u4ee5\u7528NA\u4ee3\u66ff\u3002
\npch\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u7528\u4e8e\u7ed8\u5236\u70b9\u6216\u591a\u7279\u5f81\u66fc\u54c8\u987f\u56fe\u7684\u7279\u5f81\u7684\u5f62\u72b6\u3002
\ntype\uff1a\u4e00\u4e2a\u5b57\u7b26\uff0c\u53ef\u4ee5\u662f”p”\uff08\u70b9\uff09\u3001”l”\uff08\u7ebf\uff09\u3001”h”\uff08\u5782\u76f4\u7ebf\uff09\u7b49\uff0c\u4e0e<plot>\u4e2d\u7684”type”\u53c2\u6570\u76f8\u540c\u3002
\noutward\uff1a\u4e00\u4e2a\u903b\u8f91\u503c\uff0c\u5982\u679coutward=TRUE\uff0c\u5219\u6240\u6709\u70b9\u5c06\u4ece\u5185\u90e8\u5411\u5916\u7ed8\u5236\u5706\u5f62\u66fc\u54c8\u987f\u56fe\u3002
\nLOG10\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u5c06p-value\u8f6c\u6362\u4e3alog10(p-value)\u3002<\/p>\n

@ \u66fc\u54c8\u987f\u56fe\u53c2\u6570
\ntrait.legend.ncol\uff1a\u591a\u7279\u5f81\u66fc\u54c8\u987f\u56fe\u56fe\u4f8b\u7684\u5217\u6570\u3002
\ntrait.legend.cex\uff1a\u8bbe\u7f6e\u7279\u5f81\u540d\u79f0\u56fe\u4f8b\u6587\u672c\u7684\u5927\u5c0f\u3002
\ntrait.legend.pos\uff1a\u63a7\u5236\u7279\u5f81\u540d\u79f0\u56fe\u4f8b\u5728\u56fe\u4e2d\u7684\u4f4d\u7f6e\uff0c\u6709\u4e09\u4e2a\u9009\u9879\uff1a”left”\u3001”middle”\u3001”right”\u53ef\u7528\u3002<\/p>\n

@ QQ\u56fe\u53c2\u6570
\nconf.int\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u5728QQ\u56fe\u4e0a\u7ed8\u5236\u7f6e\u4fe1\u533a\u95f4\u3002
\nconf.int.col\uff1a\u5b57\u7b26\u6216\u5411\u91cf\uff0cQQ\u56fe\u7f6e\u4fe1\u533a\u95f4\u7684\u989c\u8272\u3002<\/p>\n

@ \u5bc6\u5ea6\u56fe\u53c2\u6570
\nbin.size\uff1aSNP_density\u7ed8\u56fe\u7684bin\u5927\u5c0f\u3002
\nbin.range\uff1a\u4e00\u4e2a\u5411\u91cf\uff0cc(min, max)\uff0c\u8868\u793aSNP_density\u7ed8\u56fe\u7684\u6700\u5c0f\/\u6700\u5927\u503c\u3002\u5c0f\u4e8e\/\u5927\u4e8e’bin.range’\u7684SNP\u6570\u5c06\u4f7f\u7528\u76f8\u540c\u7684\u989c\u8272\u3002
\nbin.legend.num\uff1aSNP\u5bc6\u5ea6\u56fe\u56fe\u4f8b\u7684\u65ad\u70b9\u6570\u91cf\uff0c\u9ed8\u8ba4\u4e3a10\u3002<\/p>\n

@ \u5750\u6807\u8f74
\nylim\uff1a\u5411\u91cf\u6216\u5217\u8868\uff0cCMplot\u53ea\u4f1a\u5728\u6b64\u95f4\u9694\u5185\u7ed8\u5236\u70b9\uff0cylim\u53ef\u4ee5\u662f\u5411\u91cf\u6216\u5217\u8868\uff0c\u5982\u679c\u662f\u5217\u8868\uff0c\u4e0d\u540c\u7279\u5f81\u53ef\u4ee5\u5206\u914d\u4e0d\u540c\u7684y\u8f74\u8303\u56f4\u3002
\ncex.axis\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u63a7\u5236X\/Y\u8f74\u523b\u5ea6\u6807\u7b7e\u7684\u5927\u5c0f\u548c\u5706\u5f62\u56fe\u7684\u67d3\u8272\u4f53\u6807\u7b7e\u7684\u5927\u5c0f\u3002
\nlwd.axis\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u63a7\u5236X\/Y\u8f74\u7ebf\u7684\u7c97\u7ec6\u3002
\ncex.lab\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u63a7\u5236X\/Y\u8f74\u6807\u7b7e\u7684\u5927\u5c0f\u3002
\nylab\uff1a\u4e00\u4e2a\u5b57\u7b26\uff0cy\u8f74\u7684\u6807\u7b7e\u3002
\nylab.pos\uff1aylab\u548cy\u8f74\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002
\nxticks.pos\uff1ax\u8f74\u523b\u5ea6\u6807\u7b7e\u548cx\u8f74\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002<\/p>\n

@ \u6807\u9898\u53c2\u6570
\nmain\uff1a\u5b57\u7b26\u6216\u5411\u91cf\uff0c\u66fc\u54c8\u987f\u56fe\u548cQQ\u56fe\u7684\u6807\u9898\u3002
\nmain.cex\uff1a\u6807\u9898\u7684\u5927\u5c0f\u3002
\nmain.font\uff1a\u6807\u9898\u7684\u5b57\u4f53\u3002<\/p>\n

@ \u753b\u5e03
\nbox\uff1a\u903b\u8f91\u503c\uff0c\u6b64\u51fd\u6570\u5728\u5f53\u524d\u66fc\u54c8\u987f\u56fe\u5468\u56f4\u7ed8\u5236\u4e00\u4e2a\u6846\u3002
\nmar\uff1a\u7ed8\u56fe\u5468\u56f4\u7684\u767d\u8272\u95f4\u9694\u7684\u5927\u5c0f\uff0c\u9700\u8981\u63d0\u4f9b4\u4e2a\u503c\uff0c\u8868\u793a\u5e95\u90e8\u3001\u5de6\u4fa7\u3001\u4e0a\u65b9\u548c\u53f3\u4fa7\u7684\u95f4\u9694\u65b9\u5411\u3002<\/p>\n

@ \u9608\u503c
\nthreshold\uff1a\u4e00\u4e2a\u6570\u5b57\u3001\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u663e\u8457\u6027\u9608\u503c\u3002\u4f8b\u5982\uff0cBonferroni\u6821\u6b63\u65b9\u6cd5\uff1athreshold=0.01\/nrow(Pmap)\uff0c\u53ef\u4ee5\u5728\u7ed8\u56fe\u4e2d\u6dfb\u52a0\u591a\u6761\u663e\u8457\u6027\u7ebf\uff0c\u5982\u679c\u662f\u5217\u8868\uff0c\u5219\u53ef\u4ee5\u4e3a\u6bcf\u4e2a\u7279\u5f81\u5206\u914d\u4e0d\u540c\u7684\u9608\u503c\uff0c\u5982\u679cthreshold=0\u6216NULL\uff0c\u5219\u4e0d\u4f1a\u6dfb\u52a0\u9608\u503c\u7ebf\u3002
\nthreshold.col\uff1a\u4e00\u4e2a\u5b57\u7b26\u6216\u5411\u91cf\uff0c\u8868\u793a\u9608\u503c\u7ea7\u522b\u7ebf\u7684\u989c\u8272\uff0c\u4e5f\u53ef\u4ee5\u63a7\u5236Q-Q\u56fe\u7684\u5bf9\u89d2\u7ebf\u7684\u989c\u8272\u3002
\nthreshold.lwd\uff1a\u4e00\u4e2a\u6570\u5b57\u6216\u5411\u91cf\uff0c\u8868\u793a\u9608\u503c\u7ea7\u522b\u7ebf\u7684\u5bbd\u5ea6\uff0c\u4e5f\u53ef\u4ee5\u63a7\u5236Q-Q\u56fe\u7684\u5bf9\u89d2\u7ebf\u7684\u7c97\u7ec6\u3002
\nthreshold.lty\uff1a\u4e00\u4e2a\u6570\u5b57\u6216\u5411\u91cf\uff0c\u8868\u793a\u9608\u503c\u7ea7\u522b\u7ebf\u7684\u7c7b\u578b\uff0c\u4e5f\u53ef\u4ee5\u63a7\u5236Q-Q\u56fe\u7684\u5bf9\u89d2\u7ebf\u7684\u7c7b\u578b\u3002<\/p>\n

@ \u663e\u8457\u70b9
\namplify\uff1a\u903b\u8f91\u503c\uff0cCMplot\u53ef\u4ee5\u653e\u5927\u663e\u8457\u6027\u70b9\u3002\u5982\u679camplify=T\uff0c\u5219\u5927\u4e8e\u6700\u5c0f\u663e\u8457\u6c34\u5e73\u7684\u70b9\u5c06\u88ab\u653e\u5927\uff0c\u9ed8\u8ba4\u503c\uff1aamplify=TRUE\u3002
\nsignal.cex\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u5982\u679camplify=TRUE\uff0c\u5219\u53ef\u4ee5\u8bbe\u7f6e\u663e\u8457\u6027\u70b9\u7684\u5927\u5c0f\u3002
\nsignal.pch\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u5982\u679camplify=TRUE\uff0c\u5219\u53ef\u4ee5\u8bbe\u7f6e\u663e\u8457\u6027\u70b9\u7684pch\u3002
\nsignal.col\uff1a\u4e00\u4e2a\u5b57\u7b26\uff0c\u5982\u679camplify=TRUE\uff0c\u5219\u53ef\u4ee5\u8bbe\u7f6e\u663e\u8457\u6027\u70b9\u7684\u989c\u8272\uff0c\u5982\u679csignal.col=NULL\uff0c\u5219\u663e\u8457\u6027\u70b9\u7684\u989c\u8272\u4e0d\u4f1a\u6539\u53d8\u3002
\nsignal.line\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u8868\u793a\u663e\u8457\u6027SNP\u7684\u7ebf\u7684\u7c97\u7ec6\u3002
\nhighlight\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u540d\u79f0\u3002\u5411\u91cf\u7528\u4e8e\u5355\u4e2a\u7279\u5f81\uff0c\u5217\u8868\u7528\u4e8e\u591a\u4e2a\u7279\u5f81\u3002
\nhighlight.cex\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u70b9\u7684\u5927\u5c0f\u3002
\nhighlight.pch\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u70b9\u7684pch\u3002
\nhighlight.type\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u70b9\u7684\u7c7b\u578b\u3002
\nhighlight.col\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u70b9\u7684\u989c\u8272\u3002
\nhighlight.text\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u9700\u8981\u5728\u7a81\u51fa\u663e\u793a\u7684SNP\u5468\u56f4\u6dfb\u52a0\u7684\u6587\u672c\u3002
\nhighlight.text.col\uff1a\u4e00\u4e2a\u5411\u91cf\u6216\u5217\u8868\uff0c\u8868\u793a\u6dfb\u52a0\u7684\u6587\u672c\u7684\u989c\u8272\u3002
\nhighlight.text.cex\uff1a\u4e00\u4e2a\u503c\uff0c\u8868\u793a\u6dfb\u52a0\u7684\u6587\u672c\u7684\u5927\u5c0f\u3002
\nhighlight.text.xadj\uff1a\u5bf9\u4e8e\u5355\u4e2a\u7279\u5f81\u7684\u503c\u6216\u5411\u91cf\uff0c\u5bf9\u4e8e\u591a\u4e2a\u7279\u5f81\u7684\u5217\u8868\uff0c\u63a7\u5236\u6587\u672c\u5728\u7a81\u51fa\u663e\u793a\u7684SNP\u5468\u56f4\u7684\u4f4d\u7f6e\uff0c-1\uff08\u5de6\uff09\uff0c0\uff08\u4e2d\u5fc3\uff09\uff0c1\uff08\u53f3\uff09\u3002
\nhighlight.text.yadj\uff1a\u5bf9\u4e8e\u5355\u4e2a\u7279\u5f81\u7684\u503c\u6216\u5411\u91cf\uff0c\u5bf9\u4e8e\u591a\u4e2a\u7279\u5f81\u7684\u5217\u8868\uff0c\u63a7\u5236\u6587\u672c\u5728\u7a81\u51fa\u663e\u793a\u7684SNP\u5468\u56f4\u7684\u4f4d\u7f6e\uff0c-1\uff08\u5411\u4e0b\uff09\uff0c0\uff08\u4e2d\u5fc3\uff09\uff0c1\uff08\u5411\u4e0a\uff09\u3002
\nhighlight.text.font\uff1a\u7a81\u51fa\u663e\u793a\u7684SNP\u7684\u6587\u672c\u5b57\u4f53\u3002<\/p>\n

@ \u67d3\u8272\u4f53\u76f8\u5173\u53c2\u6570
\nchr.labels\uff1a\u4e00\u4e2a\u5411\u91cf\uff0c\u8868\u793a\u5bc6\u5ea6\u56fe\u548c\u5706\u5f62\u66fc\u54c8\u987f\u56fe\u7684\u67d3\u8272\u4f53\u6807\u7b7e\u3002
\nchr.border\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u5728\u67d3\u8272\u4f53\u4e4b\u95f4\u7ed8\u5236\u70b9\u7ebf\u3002
\nchr.labels.angle\uff1a\u4e00\u4e2a\u503c\uff0c\u8c03\u6574\u66fc\u54c8\u987f\u56fex\u8f74\u523b\u5ea6\u6807\u7b7e\u7684\u89d2\u5ea6\uff08-90 < chr.labels.angle < 90\uff09\u3002
\nchr.pos.max\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u5c06\u6bcf\u4e2a\u67d3\u8272\u4f53\u7684\u7269\u7406\u4f4d\u7f6e\u5305\u542b\u5728\u67d3\u8272\u4f53\u7684\u6700\u5927\u957f\u5ea6\u5185\u3002
\nchr.den.col\uff1a\u4e00\u4e2a\u5b57\u7b26\u3001\u5411\u91cf\u6216NULL\uff0c\u8868\u793aSNP\u5bc6\u5ea6\u7684\u989c\u8272\u3002\u5982\u679c\u53c2\u6570’chr.den.col’\u7684\u957f\u5ea6\u5927\u4e8e1\uff0c\u5219\u4f1a\u5728\u5706\u5f62\u56fe\u7684\u5e95\u90e8\u7ed8\u5236\u8ba1\u7b97\u7ed9\u5b9a\u5927\u5c0f\uff08’bin.size’\uff09\u5185\u7684SNP\u6570\u91cf\u7684SNP\u5bc6\u5ea6\u3002\u5982\u679cchr.den.col=NULL\uff0c\u5219\u4e0d\u4f1a\u5728\u66fc\u54c8\u987f\u56fe\u5e95\u90e8\u9644\u52a0\u5bc6\u5ea6\u6761\u3002
\ncir.band\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u8868\u793a\u5706\u4e4b\u95f4\u7684\u95f4\u8ddd\uff0c\u9ed8\u8ba4\u4e3a1\u3002
\ncir.chr\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u5728\u5706\u7684\u5468\u8fb9\u7ed8\u5236\u8868\u793a\u67d3\u8272\u4f53\u7684\u8fb9\u754c\uff0c\u9ed8\u8ba4\u4e3aTRUE\u3002
\ncir.chr.h\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u8868\u793a\u8fb9\u754c\u7684\u5bbd\u5ea6\uff0c\u5982\u679ccir.chr=FALSE\uff0c\u5219\u6b64\u53c2\u6570\u65e0\u6548\u3002
\ncir.legend\uff1a\u903b\u8f91\u503c\uff0c\u662f\u5426\u6dfb\u52a0\u6bcf\u4e2a\u5706\u7684\u56fe\u4f8b\u3002
\ncir.legend.cex\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c\u56fe\u4f8b\u6587\u672c\u7684\u5927\u5c0f\u3002
\ncir.legend.col\uff1a\u4e00\u4e2a\u5b57\u7b26\uff0c\u56fe\u4f8b\u8f74\u7684\u989c\u8272\u3002<\/p>\n

@ \u6587\u4ef6\u8f93\u51fa\u53c2\u6570
\nfile.output\uff1a\u903b\u8f91\u503c\uff0c\u7528\u6237\u53ef\u4ee5\u9009\u62e9\u662f\u5426\u8f93\u51fa\u7ed8\u56fe\u7ed3\u679c\u3002
\nfile.name\uff1a\u5b57\u7b26\u6216\u5411\u91cf\uff0c\u8f93\u51fa\u6587\u4ef6\u7684\u540d\u79f0\u3002
\nfile\uff1a\u5b57\u7b26\uff0c\u7528\u6237\u53ef\u4ee5\u9009\u62e9\u7ed8\u56fe\u7684\u4e0d\u540c\u8f93\u51fa\u683c\u5f0f\uff0c\u76ee\u524d\u652f\u6301”jpg”\u3001”pdf”\u3001”tiff”\u3002
\ndpi\uff1a\u4e00\u4e2a\u6570\u5b57\uff0c.jpg\u548c.tiff\u6587\u4ef6\u7684\u56fe\u7247\u5206\u8fa8\u7387\uff0c\u9ed8\u8ba4\u4e3a300\u3002
\nheight\uff1a\u8f93\u51fa\u6587\u4ef6\u7684\u9ad8\u5ea6\u3002
\nwidth\uff1a\u8f93\u51fa\u6587\u4ef6\u7684\u5bbd\u5ea6\u3002
\nverbose\uff1a\u662f\u5426\u6253\u5370\u65e5\u5fd7\u4fe1\u606f\u3002<\/p>\n

<\/a>SNP\u5bc6\u5ea6\u56fe<\/h2>\n

<\/p>\n

<\/a>\u5355\u6027\u72b6\u66fc\u54c8\u987f\u56fe<\/h2>\n

CMplot(cattle50K, plot.type = “m”,
\ncol= c(“#3E0A52”, “#423D77″,”#3F678B”,
\n“#468C8D”, “#5FB47F”, “#9FD55C”,”#F9E956″), cex = 0.5,
\nthreshold = c(0.01,0.05)\/nrow(cattle50K),
\nthreshold.col = c(‘green’,’darkgreen’),threshold.lty = c(1,2),threshold.lwd = c(1,1),
\namplify = T, signal.cex = c(1.5,1.5), signal.pch = c(18,18),signal.col = c(“red”,”skyblue”),
\nchr.den.col = c(“darkgreen”,”yellow”,”red”), # \u5728\u66fc\u54c8\u987f\u56fe\u4e2d\u6dfb\u52a0SNP\u5bc6\u5ea6\u56fe
\nfile.output = F)<\/p>\n

<\/p>\n

<\/p>\n

<\/p>\n

<\/a>\u591a\u6027\u72b6\u66fc\u54c8\u987f\u56fe<\/h2>\n

CMplot(cattle50K, plot.type = “m”, cex = 0.5, r = 0.5, threshold = c(0.01,0.05)\/nrow(cattle50K),
\nthreshold.col = c(‘green’,’darkgreen’),threshold.lty = c(1,2),threshold.lwd = c(1,1),
\namplify = T, multracks = T, signal.cex = c(1,1), signal.pch = c(18,18),signal.col = c(“red”,”skyblue”),
\nfile.output = F)<\/p>\n

<\/p>\n

<\/p>\n

<\/p>\n

\u4ece\u8fd9\u4e2a\u56fe\u4e2d\u6211\u4eec\u53ef\u4ee5\u770b\u51fa\u591a\u6027\u72b6\u7684\u6f2b\u753b\u56fe\u6bd4\u8f83\u6742\u4e71\uff0c\u666e\u901a\u7684\u66fc\u54c8\u987f\u56fe\u4e0d\u9002\u5408\u5c55\u793a\u591a\u6027\u72b6\u7684GWAS\u7ed3\u679c\u3002\u4f46\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u73af\u5f62\u66fc\u54c8\u987f\u56fe\uff01<\/p>\n

<\/a>\u73af\u5f62\u66fc\u54c8\u987f\u56fe<\/h2>\n

CMplot(cattle50K, plot.type=”c”, r=0.5, threshold=c(0.01,0.05)\/nrow(cattle50K), cex = 0.5,
\nthreshold.col = c(‘green’,’darkgreen’),threshold.lty = c(1,2),threshold.lwd = c(1,1),
\namplify = T, cir.chr.h = 2,
\nsignal.cex = c(1,1), signal.pch = c(18,18),signal.col = c(“red”,”skyblue”),file.output = F)<\/p>\n

<\/p>\n

<\/a>\u7ed8\u5236QQ plot<\/h2>\n

CMplot(cattle50K,plot.type = “q”,multracks = T, threshold = 0.05, threshold.col = “red”,
\namplify = T,signal.cex = 1.5, signal.pch = 20, signal.col = “skyblue”,
\nfile.output = F)<\/p>\n

<\/p>\n

<\/p>\n

\u5b66\u4f1a\u4f7f\u7528CMplot\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u7b80\u5355\u5feb\u6377\u7684\u7ed8\u5236\u51fa\u7cbe\u7f8e\u7684\u66fc\u54c8\u987f\u56fe\uff0c\u5f53\u6211\u4eec\u9047\u5230\u5f88\u591a\u53c2\u6570\u7684\u65f6\u5019\u4e0d\u8981\u5bb3\u6015\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u6559\u5927\u5bb6\u4e00\u4e2a\u5c0f\u6280\u5de7\u2013\u4e0d\u505c\u7684\u53bb\u8bd5\uff0c\u5927\u80c6\u7684\u53bb\u4fee\u6539\u53c2\u6570\uff0c\u8fd9\u6837\u8fc7\u540e\uff0c\u81ea\u7136\u800c\u7136\u5730\u5c31\u77e5\u9053\u6bcf\u4e2a\u53c2\u6570\u7684\u610f\u4e49\u5566\uff01<\/p>\n

\u597d\u5566\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566\uff01\u5e0c\u671b\u4eca\u5929\u5c0f\u679c\u7684\u5206\u4eab\u53ef\u4ee5\u5e2e\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ca\u65f6\u7684\u8ddf\u968f\u7814\u7a76\u7684\u70ed\u70b9\u54e6~\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<\/a>)<\/p>\n","protected":false},"excerpt":{"rendered":"

\u5728\u6700\u8fd1\u7684\u8fd9\u6bb5\u65f6\u95f4\u91cc\u76f8\u4fe1\u505a\u79d1\u7814\u7684\u5404\u4f4d\u5c0f\u4f19\u4f34\u90fd\u88abGWAS\u548c\u5b5f\u5fb7\u5c14\u968f\u673a\u5316\u5237\u8fc7\u5c4f\uff0c\u5c0f\u679c\u4e5f\u6709\u5728\u505a\u6559\u5b66\u7684\u63a8\u6587\u54e6~\u6709\u5174\u8da3\u7684\u5c0f […]<\/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\/26280"}],"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=26280"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26280\/revisions"}],"predecessor-version":[{"id":26292,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26280\/revisions\/26292"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26280"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26280"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26280"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}