{"id":26263,"date":"2024-01-25T12:15:18","date_gmt":"2024-01-25T04:15:18","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26263"},"modified":"2024-01-25T12:15:19","modified_gmt":"2024-01-25T04:15:19","slug":"%e4%bf%9d%e5%a7%86%e7%ba%a7%e6%95%99%e7%a8%8b%ef%bc%81%ef%bc%81%e5%b0%8f%e6%9e%9c%e6%95%99%e4%bd%a0%e5%ad%a6%e4%b9%a0%e6%9b%bc%e5%93%88%e9%a1%bf%e5%9b%be%ef%bc%81manhattan%e5%9b%be%ef%bc%81%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26263","title":{"rendered":"\u4fdd\u59c6\u7ea7\u6559\u7a0b\uff01\uff01\u5c0f\u679c\u6559\u4f60\u5b66\u4e60\u66fc\u54c8\u987f\u56fe\uff01Manhattan\u56fe\uff01\uff01"},"content":{"rendered":"

\u6709\u7684\u5c0f\u4f19\u4f34\u53ef\u80fd\u542c\u8bf4\u8fc7\u66fc\u54c8\u987f\u56fe\uff0c\u4f46\u662f\u5e76\u4e0d\u4e86\u89e3\uff0c\u4e5f\u4e0d\u77e5\u9053\u662f\u6765\u505a\u4ec0\u4e48\u7684\uff0c\u5176\u5b9e\uff0c\u66fc\u54c8\u987f\u56e0\u4e3a\u5176\u5f62\u4f3c\u66fc\u54c8\u987f\u6469\u5929\u5927\u697c\uff0c\u6240\u4ee5\u88ab\u79f0\u4e3a\u66fc\u54c8\u987f\u56fe\u3002\u672c\u8d28\u4e0a\u5c31\u662f\u6563\u70b9\u56fe\uff0c\u6211\u4eec\u4e00\u822c\u7528\u6765\u5c55\u793a\u5927\u91cf\u975e\u96f6\u7684\u6ce2\u52a8\u6570\u636e\u3002Y\u8f74\u9ad8\u70b9\u662f\u7528\u6765\u663e\u793a\u5177\u6709\u76f8\u5173\u6027\u7684\u4f4d\u70b9\u3002\u5e73\u65f6\u6211\u4eec\u7528\u7684\u6700\u591a\u7684\u5c31\u662f\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u5206\u6790\u7814\u7a76\u4e2d\u4e5f\u5c31\u662fGWAS\uff0c\u56e0\u4e3a\u66fc\u54c8\u987f\u56fe\u53ef\u4ee5\u4e00\u76ee\u4e86\u7136\u7684\u67e5\u770b\u57fa\u56e0\u7684\u9891\u7387\u548c\u5206\u5e03\u3002<\/p>\n

\u5c0f\u4f19\u4f34\u662f\u4e0d\u662f\u4e86\u89e3\u4e86\u5f88\u591a\uff0c\u4e0b\u9762\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u53bb\u5b66\u4e60\u4e00\u4e0b\u5982\u4f55\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\u3002<\/p>\n

\u66fc\u54c8\u987f\u56fe\u7ed8\u5236\u65b9\u6cd5\u6709\u5f88\u591a\u79cd\uff0c\u4eca\u5929\u5c31\u5e26\u5927\u5bb6\u4e86\u89e3\u4e00\u4e0b\uff1a<\/p>\n

install.packages(‘qqman’)<\/p>\n

library(qqman)#\u8fd9\u91cc\u4e3b\u8981\u7528\u5230qqman\u8fd9\u4e2aR\u5305\uff0c\u8fd9\u4e2a\u5f88\u597d\u4e0b\u8f7d\uff0c\u666e\u901a\u65b9\u5f0f\u5c31\u53ef\u4ee5\u4e0b\u8f7d\u3002<\/p>\n

\u8fd9\u91cc\u6211\u4eec\u4f7f\u7528R\u5305qqman\u81ea\u5e26\u7684\u5b9e\u4f8b\u6570\u636e\u96c6qwas \u53bb\u4e3a\u5927\u5bb6\u5c55\u793a\uff0c<\/p>\n

<\/p>\n

\u5c0f\u4f19\u4f34\u53ef\u4ee5\u6309\u7167\u8fd9\u4e2a\u5f62\u5f0f\u53bb\u8bbe\u7f6e\u81ea\u5df1\u7684\u6570\u636e<\/p>\n

\u5176\u4e2dSNP\u662fsnp\u540d\u79f0\uff0cCHR\u662f\u67d3\u8272\u4f53\u7684\u7f16\u53f7\uff0cBP\u662f\u78b1\u57fa\u7684\u4f4d\u7f6e\uff0cP\u5c31\u662fP\u503c\u5566<\/p>\n

\u6211\u4eec\u5148\u7ed8\u5236\u7b80\u5355\u7684\u66fc\u54c8\u987f\u56femanhattan\uff1a<\/p>\n

manhattan(gwasResults, col = c(“blue4”, “orange3”), main = “Results from simulated trait”,genomewideline = FALSE, suggestiveline = FALSE,highlight = snpsOfInterest[1:10])<\/p>\n

<\/p>\n

\u4f46\u662f\u8fd9\u4e2a\u56fe\u770b\u8d77\u6765\u5e73\u5e73\u65e0\u5947\uff0c\u6211\u4eec\u52a0\u70b9\u7ec6\u8282\uff0c\u52a0\u5165\u6807\u9898\uff0c\u8c03\u6574\u989c\u8272\uff0c\u628a\u90e8\u5206SNP\u9ad8\u4eae\u7b49\u4e00\u4e9b\u7ec6\u8282\u3002<\/p>\n

head(snpOfInterest) #\u8fd9\u91cc\u6211\u4eec\u5148\u67e5\u770b\u5185\u7f6e\u9ad8\u4eaesnp\u6570\u636e\uff0c snpOfInterest\u53ef\u81ea\u884c\u8bbe\u7f6e<\/p>\n

manhattan(gwasResults, col = c(“blue4”, “orange3”), main = “Results from simulated trait”,genomewideline = FALSE, suggestiveline = FALSE,highlight = snpsOfInterest[1:10])<\/p>\n

<\/p>\n

\u91cc\u9762\u53c2\u6570 CHR3\u7684\u7eff\u70b9\u662f\u6765\u81easnpsOflnterest,highlight\u53c2\u6570\u63a7\u5236\u3002<\/p>\n

\u84dd\u8272\u6a2a\u7ebf\u662f\u7531\u53c2\u6570suggestiveline\u63a7\u5236\uff0c\u7ea2\u8272\u4f7f\u7528genomewideline\u63a7\u5236<\/p>\n

\u5c0f\u4f19\u4f34\u53ef\u4ee5\u81ea\u4fe1\u8bbe\u7f6e\u3002<\/p>\n

\u6211\u4eec\u8fd8\u53ef\u4ee5\u628a\u57fa\u56e0\u540d\u52a0\u4e0a\u53bb\uff0c\u8fd9\u91cc\u6211\u4eec\u53bb\u6559\u5927\u5bb6\u5982\u4f55\u6279\u91cf\u8868\u793a\u57fa\u56e0\u540d\uff1a<\/p>\n

gwasResults[3057,1] <- “AA” #\u8fd9\u91cc\u5c06\u5c06\u6700\u663e\u8457\u7684\u70b9\uff0c\u81ea\u5b9a\u4e49\uff0c\u53ef\u770b\u51fa\u6539\u53d8<\/p>\n

manhattan(gwasResults,suggestiveline =FALSE,genomewideline =FALSE,col=c(“#FF6A6A”,”#43CD80″,”#EE7600″),annotatePval=0.05,annotateTop=TRUE)<\/p>\n

<\/p>\n

\u5c31\u7ed8\u5236\u5b8c\u6210\u4e86\uff0c\u4e0a\u8ff0\u4ee3\u7801\u4e2d\uff0cannotatePval\u53ef\u4ee5\u8bbe\u7f6ep\u9608\u503c\uff0c\u4f4e\u4e8e\u8be5\u503c\u7684\u6563\u70b9\u5c06\u4f1a\u5728\u56fe\u4e2d\u88ab\u6807\u8bb0\uff0cannotateTop\u9ed8\u8ba4\u4e3aTrue\uff0c\u5373\u4ec5\u6807\u8bb0p\u503c\u6700\u5c0f\u7684\u70b9\uff0c\u6240\u4ee5\u8be5\u56fe\u4e2d\u5404\u6761\u67d3\u8272\u4f53\u53ea\u6709\u4e00\u4e2asnp\u88ab\u6807\u8bb0\uff0c\u5018\u82e5annotateTop\u8bbe\u7f6e\u4e3aFalse\uff0c\u5219\u6240\u6709\u4f4e\u4e8eannotatePval\u7684\u70b9\u5747\u4f1a\u88ab\u6807\u8bb0\u3002<\/p>\n

\u4e0a\u8ff0\u662f\u4f7f\u7528qqman\u5305\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\uff0c\u5c0f\u679c\u8fd9\u91cc\u8fd8\u6709\u4e00\u79cd\u65b9\u6cd5\uff0cCMplot\u5305\u7ed8\u5236\u66fc\u54c8\u987f\u56fe\uff0c<\/p>\n

\u8fd9\u4e2a\u5305\u53c2\u6570\u4f1a\u66f4\u591a\uff0c\u800c\u4e14\u56fe\u4f1a\u66f4\u597d\u770b\u3002\u5e76\u4e14\u53ef\u4ee5\u7ed8\u5236\u591a\u8868\u578b\u7684\u66fc\u54c8\u987f\u56fe\uff0c\u4ee5\u53cacircos\u72b6\u5c55\u793a\u3002\u662f\u4e0d\u662f\u5f88\u5fc3\u52a8\uff0c<\/p>\n

library(CMplot)<\/p>\n

#\u6211\u4eec\u9996\u5148\u8f7d\u5165\u8fd9\u4e2a\u5305<\/p>\n

CMplot(pig60K,plot.type=”m”,LOG10=TRUE,threshold=NULL,chr.den.col=NULL,file=”jpg”,dpi=300)<\/p>\n

\u8fd9\u91cc\u4f7f\u7528\u5185\u90e8\u7684\u6570\u636e\u96c6pig60K\uff0c\u5c0f\u4f19\u4f34\u6839\u636e\u6570\u636e\u96c6\u5f62\u5f0f\u81ea\u884c\u53bb\u8bbe\u7f6e\uff1a<\/p>\n

<\/p>\n

\u8fd9\u4e2a\u56fe\u7ed8\u5236\u5b8c\u4f1a\u4f1a\u51fa\u73b0\u5728\u8bbe\u7f6e\u597d\u7684\u6587\u4ef6\u5939\u91cc\uff0c\u6765\u770b\u770b\u6548\u679c\uff1a<\/p>\n

<\/p>\n

\u6211\u4eec\u7ed8\u5236SNP\u7684\u5bc6\u5ea6\u56fe\uff1a<\/p>\n

CMplot(pig60K, plot.type=”m”, LOG10=TRUE, ylim=NULL, threshold=c(1e-6,1e-4),threshold.lty=c(1,2), threshold.lwd=c(1,1), threshold.col=c(“black”,”grey”),<\/p>\n

amplify=TRUE,chr.den.col=c(“darkgreen”,”yellow”,”red”),bin.size=1e6,signal.col=c(“red”,”green”),signal.cex=c(1,1),signal.pch=c(19,19),file=”jpg”,dpi=300)<\/p>\n

<\/p>\n

\u63a5\u4e0b\u6765\u6211\u4eec\u8fd8\u53ef\u4ee5\u5bf9\u591a\u8868\u578b\u7684\u6570\u636e\u5c55\u793a\uff1a<\/p>\n

CMplot(pig60K, plot.type=”m”, multracks=TRUE, threshold=c(1e-6,1e<\/p>\n

4),threshold.lty=c(1,2),threshold.lwd=c(1,1), threshold.col=c(“black”,”grey”), amplify=TRUE,bin.size=1e6,chr.den.col=c(“darkgreen”, “yellow”, “red”), signal.col=c(“red”,”green”),signal.cex=c(1,1),file=”jpg”,memo=””,dpi=300)<\/p>\n

<\/p>\n

\u6211\u4eec\u8fd8\u53ef\u4ee5\u7ed8\u5236\u5708\u56fe\u4e5f\u5c31\u662fcircos\u5c55\u793a\uff1a<\/p>\n

CMplot(pig60K,plot.type=”c”,chr.labels=paste(“Chr”,c(1:18,”X”),sep=””),r=0.4,cir.legend=TRUE,outward=FALSE,cir.legend.col=”black”,cir.chr.h=1.3,chr.den.col=”black”,file=”jpg”,dpi=300)<\/p>\n

<\/p>\n

\u4e0a\u8ff0\u90fd\u662f\u4f7f\u7528\u81ea\u5e26\u7684\u793a\u4f8b\u6570\u636epig60K\uff0c\u5c0f\u679c\u8fd8\u662f\u559c\u6b22circos\u7684\u56fe\u7247\uff0c\u56fe\u7247\u597d\u770b\u7cbe\u7f8e\u3002<\/p>\n

\u4e0a\u8ff0\u5c31\u662f\u6211\u4eec\u5bf9\u66fc\u54c8\u987f\u7684\u5b66\u4e60\uff0c\u5c0f\u4f19\u4f34\u6709\u6ca1\u6709\u5b66\u4f1a\u5462\uff0c\u53bb\u51c6\u5907\u4e00\u4e0b\u81ea\u5df1\u7684\u793a\u4f8b\u6570\u636e\uff0c\u7ed8\u5236\u597d\u770b\u7684\u66fc\u54c8\u987f\u56fe\u3002\u5c0f\u679c\u8981\u63d0\u9192\u5927\u5bb6\uff0c\u8981\u591a\u591a\u7406\u89e3\u4ee3\u7801\u53c2\u6570\u7684\u610f\u4e49\uff0c\u4e0a\u8ff0\u5c0f\u679c\u5df2\u7ecf\u6807\u6ce8\u4e86\u5f88\u591a\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u6839\u636e\u81ea\u5df1\u6570\u636e\u5185\u5bb9\u5957\u7528\u8fdb\u53bb\uff0c\u4f46\u662f\u4e5f\u4e0d\u8981\u5fd8\u8bb0\u662f\u4ec0\u4e48\u542b\u4e49\uff0c\u8fd9\u6837\u624d\u80fd\u7ed8\u5236\u51fa\u81ea\u5df1\u60f3\u8981\u7684\u66fc\u54c8\u987f\u56fe\uff01<\/p>\n","protected":false},"excerpt":{"rendered":"

\u6709\u7684\u5c0f\u4f19\u4f34\u53ef\u80fd\u542c\u8bf4\u8fc7\u66fc\u54c8\u987f\u56fe\uff0c\u4f46\u662f\u5e76\u4e0d\u4e86\u89e3\uff0c\u4e5f\u4e0d\u77e5\u9053\u662f\u6765\u505a\u4ec0\u4e48\u7684\uff0c\u5176\u5b9e\uff0c\u66fc\u54c8\u987f\u56e0\u4e3a\u5176\u5f62\u4f3c\u66fc\u54c8\u987f\u6469\u5929\u5927\u697c\uff0c\u6240\u4ee5\u88ab […]<\/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\/26263"}],"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=26263"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26263\/revisions"}],"predecessor-version":[{"id":26273,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26263\/revisions\/26273"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26263"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26263"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26263"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}