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title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138222091851530242#wechat_redirect\" title=\"\u751f\u4fe1\u6709\u5173\u7edf\u8ba1\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u6709\u5173\u7edf\u8ba1<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u672c\u671f\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e00\u4e2a\u7528\u4e8eGWAS\uff08\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u5206\u6790\uff09\u7684\u5c40\u90e8\u5355\u500d\u578b\u53ef\u89c6\u5316\u7684R\u5305\uff0c\u5b83<\/span><strong><span style=\"font-size: 14px;\">2023\u5e748\u67081\u65e5<\/span><\/strong><span style=\"font-size: 14px;\">\u53d1\u8868\u5728<strong>Bioinformatics<\/strong>\u671f\u520a\u4e0a<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u7684\uff0c\u53c8\u662f\u4e00\u4e2a\u65b0\u9c9c\u51fa\u7089\u7684\u597d\u5305\uff01<\/span><\/p>\n<p><span style=\"font-size: 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14px;\">\u5b83\u901a\u8fc7\u57fa\u4e8e\u53d8\u5f02\u8fde\u9501\u914d\u7f6e\u6587\u4ef6\u7684\u5bc6\u5ea6\u5206\u6790\uff0c\u5b9e\u73b0\u5bf9\u611f\u5174\u8da3\u7684\u5c40\u90e8\u57fa\u56e0\u7ec4\u533a\u57df\u4e2d\u7684\u5355\u4f53\u578b\u7ed3\u6784\u7684\u7a33\u5065\u805a\u7c7b\u3002\u968f\u540e\uff0ccrosshap\u8fd8\u914d\u5907\u4e86\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u7528\u4e8e\u9009\u62e9\u6700\u4f73\u7684\u805a\u7c7b\u53c2\u6570\uff08\u025b\uff09\uff0c\u7136\u540e\u751f\u6210\u4e00\u4e2a\u76f4\u89c2\u7684\u56fe\u8868\uff0c\u63d0\u4f9b\u4e86\u8fde\u63a5\u53d8\u5f02\u3001\u5355\u4f53\u578b\u7ec4\u5408\u3001\u8868\u578b\u548c\u5143\u6570\u636e\u7279\u5f81\u4e4b\u95f4\u590d\u6742\u5173\u7cfb\u7684\u6982\u89c8\u3002<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u5b89\u88c5\u53ca\u7528\u5230\u7684\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u6211\u4eec\u5c06\u5206\u6790\u7684\u6570\u636e\u6765\u81ea\u7f8e\u56fd\u519c\u4e1a\u90e8\u6838\u5fc3\u6536\u96c6\u7684\u5927\u8c46\u6570\u636e\uff08Bayer\u7b49\u4eba\uff0c2021\u5e74\uff09\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u5c0f\u679c\u63a5\u4e0b\u6765\u5c06\u4f7f\u7528crosshap\uff08Marsh\u7b49\u4eba\uff0c2022\u5e74\uff09\u590d\u73b0\u79cd\u5b50\u86cb\u767dQTL\u3001cqProt-003\u7684\u5c40\u90e8\u5355\u500d\u578b\u5206\u6790\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u60a8\u53ef\u4ee5\u4ececrosshap\u793a\u4f8b\u6570\u636e\u7684figshare\u4ed3\u5e93\u4e2d\u4e0b\u8f7d\u8fd9\u4e9b\u6570\u636e\u3002<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-size: 14px;letter-spacing: 0.034em;text-align: justify;\"><em style=\"font-size: 14px;letter-spacing: 0.578px;white-space: normal;color: rgb(178, 178, 178);\"><span style=\"font-size: 13px;text-decoration: underline;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111″,\u9886\u53d6\u4ee3\u7801\uff0c\u4ee3\u7801\u7f16\u53f7\uff1a231016<\/span><\/em><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code><span class=\"code-snippet_outer\">figshare.com\/articles\/dataset\/fin_b51_173kb_only_vcf\/<span class=\"code-snippet__number\">22331167<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"devtools\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">devtools::install_github(<span class=\"code-snippet__string\">\"jacobimarsh\/crosshap\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(crosshap)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u8f93\u5165\u6570\u636e<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u4e0b\u8f7d\u6570\u636e\u540e\uff0c\u4fdd\u5b58\u5230\u5bf9\u5e94\u7684\u8def\u5f84\uff0c\u8bfb\u53d6\u5373\u53ef\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Read example data into R and standardize using helper functions<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">vcf<\/span> <- read_vcf(<span class=\"code-snippet__string\">'path\/to\/fin_b51_173kb_only.vcf'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#VCF is provided as additional argument to help assign column and row names<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LD <- read_LD(<span class=\"code-snippet__string\">'path\/to\/plink.ld'<\/span>, vcf = vcf)<\/span><\/code><code><span class=\"code-snippet_outer\">pheno <- read_pheno(<span class=\"code-snippet__string\">'path\/to\/sprot_phen.txt'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- read_metadata(<span class=\"code-snippet__string\">'path\/to\/namepopfile.txt'<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u5c40\u90e8\u5355\u500d\u578b<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u5c40\u90e8\u5355\u4f53\u578b\u6d89\u53ca\u901a\u8fc7\u5728\u611f\u5174\u8da3\u533a\u57df\u5185\u7684\u4f4d\u70b9\u4e0a\u5171\u4eab\u7684\u5355\u4f53\u578b\uff08\u7b49\u4f4d\u57fa\u56e0\u7ec4\u5408\uff09\u6765\u5206\u7c7b\u4e2a\u4f53\u3002\u5728CrossHap\u4e2d\uff0c\u5355\u4f53\u578b\u5e76\u4e0d\u662f\u7531\u5355\u4e2a\u4f4d\u70b9\u6765\u5b9a\u4e49\u7684\uff0c\u800c\u662f\u7531\u6807\u8bb0\u7ec4\uff08Marker Groups\uff09\u7684\u7b49\u4f4d\u57fa\u56e0\u7ec4\u5408\u6765\u5b9a\u4e49\u7684\u3002\u6807\u8bb0\u7ec4\u662f\u7d27\u5bc6\u8fde\u9501\u7684SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u7684\u96c6\u7fa4\uff0c\u901a\u5e38\u5728\u6574\u4e2a\u4eba\u7fa4\u4e2d\u4f5c\u4e3a\u4e00\u4e2a\u5355\u5143\u9057\u4f20\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7528\u4e8e\u6355\u83b7\u6807\u8bb0\u7ec4\u7684\u805a\u7c7b\u7b97\u6cd5\u662fDBSCAN\uff08Ester\u7b49\u4eba\uff0c1996\u5e74\uff09\uff0c\u5728CrossHap\u4e2d\u6709\u4e24\u4e2a\u4e3b\u8981\u53c2\u6570\uff1aMGmin\u548cepsilon\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">MGmin\uff08minPts\uff09\u662f\u4e00\u4e2a\u7c07\u4e2d\u5fc5\u987b\u5177\u6709\u7684\u6700\u5c0f\u94fe\u63a5SNP\u6570\uff0c\u624d\u80fd\u5c06\u5176\u5206\u7c7b\u4e3a\u6807\u8bb0\u7ec4\uff0c\u800c\u4e0d\u662f\u80cc\u666f\u566a\u58f0\u3002\u5728\u4e0b\u9762\u7684\u793a\u4f8b\u4e2d\uff08173kb\u533a\u57df\u4e2d\u76842041\u4e2aSNP\uff09\uff0cMGmin\u7b49\u4e8e30\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Add minimum Marker Group SNP count<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">MGmin<\/span> <- <span class=\"code-snippet__number\">30<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">Epsilon<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">Epsilon\u5927\u81f4\u5bf9\u5e94\u7740\u7c07\u5bc6\u5ea6\uff0c\u5f53epsilon\u589e\u52a0\u65f6\uff0c\u901a\u5e38\u4f1a\u5305\u62ec\u66f4\u591a\u7684SNP\u5728\u66f4\u591a\u7684\u6807\u8bb0\u7ec4\u4e2d\u3002\u5728\u8fd9\u4e2a\u9636\u6bb5\uff0c\u503c\u5f97\u63d0\u4f9b\u4e00\u7cfb\u5217epsilon\u503c\uff0c\u4ee5\u4fbf\u7a0d\u540e\u9009\u62e9\u6700\u4f73\u503c\u3002\u7531\u4e8e\u8fd9\u4e2a\u6570\u636e\u96c6\u5305\u542b\u5927\u91cf\u7684SNP\uff082041\u4f4d\u70b9\uff09\uff0c\u6240\u4ee5\u6211\u4eec\u5c06\u6d4b\u8bd5\u7684epsilon\u8303\u56f4\u5c06\u4f1a\u76f8\u5bf9\u8f83\u4f4e\uff080.2 – 1\uff09\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-id\">#Add<\/span> <span class=\"code-snippet__selector-tag\">list<\/span> <span class=\"code-snippet__selector-tag\">of<\/span> <span class=\"code-snippet__selector-tag\">epsilon<\/span> <span class=\"code-snippet__selector-tag\">values<\/span> <span class=\"code-snippet__selector-tag\">to<\/span> <span class=\"code-snippet__selector-tag\">run<\/span> <span class=\"code-snippet__selector-tag\">haplotyping<\/span> <span class=\"code-snippet__selector-tag\">on<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-tag\">epsilon<\/span> <<span class=\"code-snippet__selector-tag\">-<\/span> <span class=\"code-snippet__selector-tag\">c<\/span>(0<span class=\"code-snippet__selector-class\">.2<\/span>,0<span class=\"code-snippet__selector-class\">.4<\/span>,0<span class=\"code-snippet__selector-class\">.6<\/span>,0<span class=\"code-snippet__selector-class\">.8<\/span>,1)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u73b0\u5728\u8f93\u5165\u6587\u4ef6\u548c\u53c2\u6570\u5df2\u7ecf\u8bbe\u7f6e\u597d\u5566\uff0c\u662f\u65f6\u5019\u8fdb\u884c\u5355\u500d\u578b\u5206\u6790\u4e86\uff01<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\">#Run the haplotyping at all provided epsilon values<\/span><\/code><code><span class=\"code-snippet_outer\">HapObject <- run_haplotyping(vcf = vcf,<\/span><\/code><code><span class=\"code-snippet_outer\"> LD = LD,<\/span><\/code><code><span class=\"code-snippet_outer\"> pheno = pheno,<\/span><\/code><code><span class=\"code-snippet_outer\"> metadata = metadata,<\/span><\/code><code><span class=\"code-snippet_outer\"> epsilon = epsilon,<\/span><\/code><code><span class=\"code-snippet_outer\"> MGmin = MGmin)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u5982\u679c\u4e00\u5207\u987a\u5229\uff0c\u73b0\u5728\u5df2\u7ecf\u4fdd\u5b58\u4e86\u4e00\u4e2a\u5355\u4f53\u578b\u5bf9\u8c61\uff08HapObject\uff09\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u6240\u6709\u4e94\u4e2a\u63d0\u4f9b\u7684epsilon\u503c\u7684\u5355\u4f53\u578b\u7ed3\u679c\u3002\u8fd9\u4e2a\u5355\u4f53\u578b\u5bf9\u8c61\u5c06\u9700\u8981\u7528\u6765\u6784\u5efaCrossHap\u7684\u53ef\u89c6\u5316\uff08\u4ee5\u53ca\u9009\u62e9\u7684epsilon\u503c\u4ee5\u8fdb\u884c\u53ef\u89c6\u5316\uff01\uff09<\/span><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u4f18\u5316\u805a\u7c7b\u5206\u8fa8\u7387<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">Epsilon\u662fDBSCAN\u4e2d\u4e00\u4e2a\u975e\u5e38\u96be\u4ee5\u4f18\u5316\u7684\u53c2\u6570\uff0c\u8fd9\u662f\u7528\u4e8e\u5c06SNP\u805a\u7c7b\u6210CrossHap\u4e2d\u7684\u6807\u8bb0\u7ec4\uff0c\u4ee5\u8fdb\u884c\u5355\u4f53\u578b\u5206\u6790\u3002\u5e78\u8fd0\u7684\u662f\uff0ccrosshap\u6709\u4e00\u4e2aclustree\uff08Zappia\u7b49\u4eba\uff0c2018\u5e74\uff09\u5de5\u5177\uff0c\u5b83\u53ef\u4ee5\u7528\u4e8e\u603b\u7ed3\u4e0d\u540cepsilon\u503c\u4e0b\u521b\u5efa\u7684\u5355\u4f53\u578b\u5bf9\u8c61\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c\u8ba9\u6211\u4eec\u53ef\u4ee5\u9009\u62e9\u6700\u4f73\u7684epsilon\u503c\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7b2c\u4e00\u4e2a\u805a\u7c7b\u6811\u9009\u9879\u63d0\u4f9b\u4e86\u5728\u4e0d\u540cepsilon\u503c\u4e0b\u89e3\u6790\u7684\u5355\u500d\u578b\u7ec4\u7684\u53d8\u5316\u6458\u8981\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"typescript\"><code><span class=\"code-snippet_outer\">#HapObject created by `run_haplotyping`<\/span><\/code><code><span class=\"code-snippet_outer\">#Add type = 'hap' to ensure it summarizes haplotypes rather than Marker Groups<\/span><\/code><code><span class=\"code-snippet_outer\">hap_clustree <- clustree_viz(HapObject,<\/span><\/code><code><span class=\"code-snippet_outer\"> type = 'hap')<\/span><\/code><code><span class=\"code-snippet_outer\">hap_clustree<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_U4iakjc5eDY8vHXkGpZtpru38UXUtQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZTuqN9QZ4icc4A7AEZrDsIPLLqjU4iakjc5eDY8vHXkGpZtpru38UXUtQ\/640?wx_fmt=png'\" \/><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u53ef\u89c6\u5316\u5c40\u90e8\u5355\u500d\u578b<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u73b0\u5728\u6211\u4eec\u5df2\u7ecf\u5c06\u7ed3\u679c\uff08\u5355\u500d\u578b\u5bf9\u8c61\uff09\u51c6\u5907\u597d\u4e86\uff0c\u5e76\u4e14\u5df2\u7ecf\u4e3a\u6211\u4eec\u7684\u6570\u636e\u96c6\u9009\u62e9\u4e86\u6700\u4f73\u7684epsilon\u5206\u8fa8\u7387\uff0c\u662f\u65f6\u5019\u5c06\u6211\u4eec\u7684\u7ed3\u679c\u5b8c\u6574\u5730\u53ef\u89c6\u5316\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5c31\u53ef\u4ee5\u5f00\u59cb\u53d1\u73b0\u53d8\u5316\u6a21\u5f0f\u4e86!<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u5728\u5341\u5b57\u5f62\u53ef\u89c6\u5316\u4e2d\uff0c\u4e2d\u5fc3\u77e9\u9635\u663e\u793a\u4e86\u5b9a\u4e49\u6bcf\u4e2a\u5355\u500d\u578b\u7684Marker Group\u7b49\u4f4d\u57fa\u56e0\u7684\u7ec4\u5408\uff0c\u5b83\u63d0\u4f9b\u4e86\u4e00\u4e2a\u7f51\u683c\uff0c\u56f4\u7ed5\u7740\u6bcf\u4e2aMarker Group\u548c\u5355\u500d\u578b\u7ec4\u5408\u7684\u7279\u5f81\u3002\u5355\u500d\u578b\u7684\u7279\u5f81\u548c\u5206\u914d\u7ed9\u5b83\u4eec\u7684\u4e2a\u4f53\u662f\u5782\u76f4\u53ef\u89c6\u5316\u7684\uff0c\u5728\u9876\u90e8\u548c\u5e95\u90e8\u7684\u56fe\u4e2d\u6709\u7279\u5f81\u3002\u6807\u8bb0\u7ec4\u7684\u7279\u5f81\u548c\u5206\u914d\u7ed9\u5b83\u4eec\u7684snp\u6c34\u5e73\u53ef\u89c6\u5316\uff0c\u7279\u5f81\u5728\u5de6\u8fb9\u548c\u53f3\u8fb9\u7684\u56fe\u4e0a\u3002<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ziaIoVmNapImao08hNNODOEKIqDnNA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZLJs4kbnicdpUcemJIxQicGhsrqibziaIoVmNapImao08hNNODOEKIqDnNA\/640?wx_fmt=png'\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u8fd9\u4e9b\u56fe\u90fd\u662f\u4ec0\u4e48\u610f\u601d\uff1f<\/span><\/p>\n<ul class=\"list-paddingleft-1\">\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u5728\u4e2d\u592e\u77e9\u9635\u4e0a\u65b9\uff0c\u663e\u793a\u4e86\u6bcf\u79cd\u5355\u4f53\u578b\u7ec4\u5408\u7684\u4e2a\u4f53\u9891\u7387\uff0c\u8fd8\u6709\u6309\u6211\u4eec\u63d0\u4f9b\u7684\u5143\u6570\u636e\u53d8\u91cf\uff08\u9a6f\u5316\u7a0b\u5ea6\u6c34\u5e73\uff09\u8fdb\u884c\u7684\u5206\u89e3\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u4e0b\u65b9\uff0c\u7ed8\u5236\u4e86\u6bcf\u4e2a\u4e2a\u4f53\u7684\u8868\u578b\u5f97\u5206\uff08\u79cd\u5b50\u86cb\u767d\u8d28\u542b\u91cf\u767e\u5206\u6bd4\uff09\uff0c\u6bcf\u4e2a\u70b9\u4ee3\u8868\u4e00\u4e2a\u4e2a\u4f53\uff0c\u6839\u636e\u5355\u4f53\u578b\u5206\u7ec4\uff0c\u5e76\u6839\u636e\u5143\u6570\u636e\u53d8\u91cf\u8fdb\u884c\u7740\u8272\uff0c\u5c31\u50cf\u9876\u90e8\u7684\u6761\u5f62\u56fe\u4e00\u6837\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u5de6\u4fa7\uff0c\u662f\u6bcf\u4e2a\u6807\u8bb0\u7ec4\uff08MG\uff09\u7684\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u4fe1\u606f\u6458\u8981\u3002\u8fd9\u663e\u793a\u4e86\u6bcf\u4e2a\u6807\u8bb0\u7ec4\u5185\u6240\u6709SNP\u4e2d\u6b21\u8981\u7b49\u4f4d\u57fa\u56e0\u3001\u7f3a\u5931\u7b49\u4f4d\u57fa\u56e0\u3001\u6742\u5408\u5b50\u548c\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u7684\u9891\u7387\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u53f3\u4fa7\uff0c\u7ed8\u5236\u4e86\u6bcf\u4e2aSNP\u7684\u8868\u578b\u5173\u8054\uff08\u6bcf\u4e2a\u70b9\u4ee3\u8868\u4e00\u4e2aSNP\uff09\uff0c\u6839\u636e\u6807\u8bb0\u7ec4\u8fdb\u884c\u5206\u7ec4\u3002”\u8868\u578b\u5173\u8054” \u5b9e\u9645\u4e0a\u662f\u6307\u5bf9\u4e8e\u7ed9\u5b9a\u7684SNP\uff0c\u62e5\u6709\u66ff\u4ee3\u7b49\u4f4d\u57fa\u56e0\u548c\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u7684\u4e2a\u4f53\u4e4b\u95f4\u7684\u8868\u578b\u5f97\u5206\u5dee\u5f02\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u53f3\u4e0b\u89d2\u7684\u8868\u683c\u603b\u7ed3\u4e86\u5355\u4f53\u578b\u4fe1\u606f\uff0c\u7684\u8868\u683c\u603b\u7ed3\u4e86\u6807\u8bb0\u7ec4\u4fe1\u606f\u3002\u6240\u6709\u7684\u56fe\u6ce8\u90fd\u663e\u793a\u5728\u5de6\u4e0b\u89d2\u3002<\/span><\/p>\n<\/li>\n<\/ul>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u7ed3\u8bed<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u8fd9\u4e2a\u7528\u4e8eGWAS\u7684\u5c40\u90e8\u5355\u500d\u578b\u53ef\u89c6\u5316\u7684R\u5305\uff0c\u5927\u5bb6\u4e4b\u540e\u5728\u505aGWAS\u7684\u65f6\u5019\u4e0d\u8981\u5fd8\u8bb0\u8fd9\u4e2a\u5de5\u5177\u54e6\uff01<\/span><\/p>\n<h2><span style=\"font-size: 14px;\">\u53c2\u8003\u6587\u732e<\/span><\/h2>\n<p><span style=\"font-size: 14px;\">[1] Marsh JI, Petereit J, Johnston BA, Bayer PE, Tay Fernandez CG, Al-Mamun HA, Batley J, Edwards D. crosshap: R package for local haplotype visualization for trait association analysis. Bioinformatics. 2023 Aug 1;39(8):btad518. doi: 10.1093\/bioinformatics\/btad518. PMID: 37607004; PMCID: PMC10471896.<\/span><\/p>\n<p><span style=\"font-size: 14px;\">[2] <\/span><span style=\"font-size: 14px;\">https:\/\/jacobimarsh.github.io\/crosshap\/articles\/Getting_started.html<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\"><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" 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title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138222091851530242#wechat_redirect\" title=\"\u751f\u4fe1\u6709\u5173\u7edf\u8ba1\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u6709\u5173\u7edf\u8ba1<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u672c\u671f\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u4e00\u4e2a\u7528\u4e8eGWAS\uff08\u5168\u57fa\u56e0\u7ec4\u5173\u8054\u5206\u6790\uff09\u7684\u5c40\u90e8\u5355\u500d\u578b\u53ef\u89c6\u5316\u7684R\u5305\uff0c\u5b83<\/span><strong><span style=\"font-size: 14px;\">2023\u5e748\u67081\u65e5<\/span><\/strong><span style=\"font-size: 14px;\">\u53d1\u8868\u5728<strong>Bioinformatics<\/strong>\u671f\u520a\u4e0a<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u7684\uff0c\u53c8\u662f\u4e00\u4e2a\u65b0\u9c9c\u51fa\u7089\u7684\u597d\u5305\uff01<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u65e0\u8bba\u4f60\u662f\u672c\u79d1\u751f\u8fd8\u662f\u7814\u7a76\u751f\uff0c\u65e0\u8bba\u4f60\u4e13\u653b\u6e7f\u8bd5\u9a8c\u8fd8\u662f\u751f\u4fe1\uff0c\u8fd9\u7bc7\u63a8\u6587\u5c06\u4e3a\u4f60\u63d0\u4f9b\u6df1\u5165\u4e86\u89e3\u8fd9\u4e00\u4ee4\u4eba\u6fc0\u52a8\u7684\u65b0\u6280\u672f\u7684\u673a\u4f1a\u3002\u8ba9\u6211\u4eec\u4e00\u8d77\u63a2\u7d22\u4ea4\u53c9\u5355\u4f53\u578b\u805a\u7c7b\uff08crosshap\uff09\u5982\u4f55\u6539\u53d8\u6211\u4eec\u5bf9\u9057\u4f20\u5b66\u7684\u8ba4\u8bc6\uff0c\u4ee5\u53ca\u5b83\u5728\u672a\u6765\u7684\u7814\u7a76\u4e2d\u53ef\u80fd\u53d1\u6325\u7684\u4f5c\u7528\u3002\u8bf7\u770b\u5c0f\u679c\u4e0b\u9762\u7684\u5206\u4eab\uff01<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u524d\u8a00<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\">GWAS\u6280\u672f\u4ee5\u5176\u51fa\u8272\u7684\u6027\u80fd\uff0c\u6210\u529f\u5730\u5229\u7528\u4e86\u5927\u89c4\u6a21\u7684\u57fa\u56e0\u53d8\u5f02\u6570\u636e\u96c6\uff0c\u4ee5\u8bc6\u522b\u53ef\u80fd\u5bfc\u81f4\u7279\u5b9a\u8868\u578b\u7684\u5019\u9009\u533a\u57df\u3002\u7136\u800c\uff0c\u4f20\u7edf\u7684GWAS\u548c\u7cbe\u7ec6\u5b9a\u4f4d\u65b9\u6cd5\u65e0\u6cd5\u6df1\u5165\u4e86\u89e3\u5305\u542b\u5e76\u53d7\u5230\u5bfc\u81f4\u6027\u72b6\u53d8\u5f02\u7684\u9057\u4f20\u53d8\u5f02\u5f71\u54cd\u7684\u5c40\u90e8\u8fde\u9501\u57fa\u56e0\u7ec4\u7ed3\u6784\u3002<br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u5c0f\u679c\u5c06\u5e26\u9886\u5927\u5bb6\u63a2\u8ba8\u4e00\u9879\u4ee4\u4eba\u6fc0\u52a8\u7684\u65b0\u6280\u672f – crosshap\uff0c\u5b83\u4e3a\u6211\u4eec\u63d0\u4f9b\u4e86\u4e00\u79cd\u66f4\u6df1\u5165\u4e86\u89e3\u57fa\u56e0\u7ec4\u5185\u90e8\u590d\u6742\u7ed3\u6784\u7684\u65b9\u6cd5\u3002\u4f20\u7edf\u7684GWAS\u53ef\u80fd\u5df2\u7ecf\u4e3a\u6211\u4eec\u63ed\u793a\u4e86\u4e00\u4e9b\u5173\u4e8e\u57fa\u56e0\u548c\u8868\u578b\u4e4b\u95f4\u7684\u8054\u7cfb\uff0c\u4f46crosshap\u5e26\u6765\u4e86\u4e00\u79cd\u5168\u65b0\u7684\u89c6\u89d2\uff0c\u8ba9\u6211\u4eec\u80fd\u591f\u66f4\u8be6\u7ec6\u5730\u63a2\u7a76\u57fa\u56e0\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u4ee5\u53ca\u5b83\u4eec\u5982\u4f55\u5f71\u54cd\u6211\u4eec\u7684\u9057\u4f20\u7279\u5f81\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u5b83\u901a\u8fc7\u57fa\u4e8e\u53d8\u5f02\u8fde\u9501\u914d\u7f6e\u6587\u4ef6\u7684\u5bc6\u5ea6\u5206\u6790\uff0c\u5b9e\u73b0\u5bf9\u611f\u5174\u8da3\u7684\u5c40\u90e8\u57fa\u56e0\u7ec4\u533a\u57df\u4e2d\u7684\u5355\u4f53\u578b\u7ed3\u6784\u7684\u7a33\u5065\u805a\u7c7b\u3002\u968f\u540e\uff0ccrosshap\u8fd8\u914d\u5907\u4e86\u53ef\u89c6\u5316\u5de5\u5177\uff0c\u7528\u4e8e\u9009\u62e9\u6700\u4f73\u7684\u805a\u7c7b\u53c2\u6570\uff08\u025b\uff09\uff0c\u7136\u540e\u751f\u6210\u4e00\u4e2a\u76f4\u89c2\u7684\u56fe\u8868\uff0c\u63d0\u4f9b\u4e86\u8fde\u63a5\u53d8\u5f02\u3001\u5355\u4f53\u578b\u7ec4\u5408\u3001\u8868\u578b\u548c\u5143\u6570\u636e\u7279\u5f81\u4e4b\u95f4\u590d\u6742\u5173\u7cfb\u7684\u6982\u89c8\u3002<\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u5b89\u88c5\u53ca\u7528\u5230\u7684\u6570\u636e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u6211\u4eec\u5c06\u5206\u6790\u7684\u6570\u636e\u6765\u81ea\u7f8e\u56fd\u519c\u4e1a\u90e8\u6838\u5fc3\u6536\u96c6\u7684\u5927\u8c46\u6570\u636e\uff08Bayer\u7b49\u4eba\uff0c2021\u5e74\uff09\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u5c0f\u679c\u63a5\u4e0b\u6765\u5c06\u4f7f\u7528crosshap\uff08Marsh\u7b49\u4eba\uff0c2022\u5e74\uff09\u590d\u73b0\u79cd\u5b50\u86cb\u767dQTL\u3001cqProt-003\u7684\u5c40\u90e8\u5355\u500d\u578b\u5206\u6790\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\">\u60a8\u53ef\u4ee5\u4ececrosshap\u793a\u4f8b\u6570\u636e\u7684figshare\u4ed3\u5e93\u4e2d\u4e0b\u8f7d\u8fd9\u4e9b\u6570\u636e\u3002<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-size: 14px;letter-spacing: 0.034em;text-align: justify;\"><em style=\"font-size: 14px;letter-spacing: 0.578px;white-space: normal;color: rgb(178, 178, 178);\"><span style=\"font-size: 13px;text-decoration: underline;\">\u516c\u4f17\u53f7\u540e\u53f0\u56de\u590d\u201c111″,\u9886\u53d6\u4ee3\u7801\uff0c\u4ee3\u7801\u7f16\u53f7\uff1a231016<\/span><\/em><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cpp\"><code><span class=\"code-snippet_outer\">figshare.com\/articles\/dataset\/fin_b51_173kb_only_vcf\/<span class=\"code-snippet__number\">22331167<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">install.packages(<span class=\"code-snippet__string\">\"devtools\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">devtools::install_github(<span class=\"code-snippet__string\">\"jacobimarsh\/crosshap\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(crosshap)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u8f93\u5165\u6570\u636e<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u4e0b\u8f7d\u6570\u636e\u540e\uff0c\u4fdd\u5b58\u5230\u5bf9\u5e94\u7684\u8def\u5f84\uff0c\u8bfb\u53d6\u5373\u53ef\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Read example data into R and standardize using helper functions<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">vcf<\/span> <- read_vcf(<span class=\"code-snippet__string\">'path\/to\/fin_b51_173kb_only.vcf'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#VCF is provided as additional argument to help assign column and row names<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">LD <- read_LD(<span class=\"code-snippet__string\">'path\/to\/plink.ld'<\/span>, vcf = vcf)<\/span><\/code><code><span class=\"code-snippet_outer\">pheno <- read_pheno(<span class=\"code-snippet__string\">'path\/to\/sprot_phen.txt'<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">metadata <- read_metadata(<span class=\"code-snippet__string\">'path\/to\/namepopfile.txt'<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u5c40\u90e8\u5355\u500d\u578b<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u5c40\u90e8\u5355\u4f53\u578b\u6d89\u53ca\u901a\u8fc7\u5728\u611f\u5174\u8da3\u533a\u57df\u5185\u7684\u4f4d\u70b9\u4e0a\u5171\u4eab\u7684\u5355\u4f53\u578b\uff08\u7b49\u4f4d\u57fa\u56e0\u7ec4\u5408\uff09\u6765\u5206\u7c7b\u4e2a\u4f53\u3002\u5728CrossHap\u4e2d\uff0c\u5355\u4f53\u578b\u5e76\u4e0d\u662f\u7531\u5355\u4e2a\u4f4d\u70b9\u6765\u5b9a\u4e49\u7684\uff0c\u800c\u662f\u7531\u6807\u8bb0\u7ec4\uff08Marker Groups\uff09\u7684\u7b49\u4f4d\u57fa\u56e0\u7ec4\u5408\u6765\u5b9a\u4e49\u7684\u3002\u6807\u8bb0\u7ec4\u662f\u7d27\u5bc6\u8fde\u9501\u7684SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u7684\u96c6\u7fa4\uff0c\u901a\u5e38\u5728\u6574\u4e2a\u4eba\u7fa4\u4e2d\u4f5c\u4e3a\u4e00\u4e2a\u5355\u5143\u9057\u4f20\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7528\u4e8e\u6355\u83b7\u6807\u8bb0\u7ec4\u7684\u805a\u7c7b\u7b97\u6cd5\u662fDBSCAN\uff08Ester\u7b49\u4eba\uff0c1996\u5e74\uff09\uff0c\u5728CrossHap\u4e2d\u6709\u4e24\u4e2a\u4e3b\u8981\u53c2\u6570\uff1aMGmin\u548cepsilon\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">MGmin\uff08minPts\uff09\u662f\u4e00\u4e2a\u7c07\u4e2d\u5fc5\u987b\u5177\u6709\u7684\u6700\u5c0f\u94fe\u63a5SNP\u6570\uff0c\u624d\u80fd\u5c06\u5176\u5206\u7c7b\u4e3a\u6807\u8bb0\u7ec4\uff0c\u800c\u4e0d\u662f\u80cc\u666f\u566a\u58f0\u3002\u5728\u4e0b\u9762\u7684\u793a\u4f8b\u4e2d\uff08173kb\u533a\u57df\u4e2d\u76842041\u4e2aSNP\uff09\uff0cMGmin\u7b49\u4e8e30\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">#Add minimum Marker Group SNP count<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__attribute\">MGmin<\/span> <- <span class=\"code-snippet__number\">30<\/span><\/span><\/code><\/pre>\n<\/section>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">Epsilon<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">Epsilon\u5927\u81f4\u5bf9\u5e94\u7740\u7c07\u5bc6\u5ea6\uff0c\u5f53epsilon\u589e\u52a0\u65f6\uff0c\u901a\u5e38\u4f1a\u5305\u62ec\u66f4\u591a\u7684SNP\u5728\u66f4\u591a\u7684\u6807\u8bb0\u7ec4\u4e2d\u3002\u5728\u8fd9\u4e2a\u9636\u6bb5\uff0c\u503c\u5f97\u63d0\u4f9b\u4e00\u7cfb\u5217epsilon\u503c\uff0c\u4ee5\u4fbf\u7a0d\u540e\u9009\u62e9\u6700\u4f73\u503c\u3002\u7531\u4e8e\u8fd9\u4e2a\u6570\u636e\u96c6\u5305\u542b\u5927\u91cf\u7684SNP\uff082041\u4f4d\u70b9\uff09\uff0c\u6240\u4ee5\u6211\u4eec\u5c06\u6d4b\u8bd5\u7684epsilon\u8303\u56f4\u5c06\u4f1a\u76f8\u5bf9\u8f83\u4f4e\uff080.2 – 1\uff09\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-id\">#Add<\/span> <span class=\"code-snippet__selector-tag\">list<\/span> <span class=\"code-snippet__selector-tag\">of<\/span> <span class=\"code-snippet__selector-tag\">epsilon<\/span> <span class=\"code-snippet__selector-tag\">values<\/span> <span class=\"code-snippet__selector-tag\">to<\/span> <span class=\"code-snippet__selector-tag\">run<\/span> <span class=\"code-snippet__selector-tag\">haplotyping<\/span> <span class=\"code-snippet__selector-tag\">on<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-tag\">epsilon<\/span> <<span class=\"code-snippet__selector-tag\">-<\/span> <span class=\"code-snippet__selector-tag\">c<\/span>(0<span class=\"code-snippet__selector-class\">.2<\/span>,0<span class=\"code-snippet__selector-class\">.4<\/span>,0<span class=\"code-snippet__selector-class\">.6<\/span>,0<span class=\"code-snippet__selector-class\">.8<\/span>,1)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u73b0\u5728\u8f93\u5165\u6587\u4ef6\u548c\u53c2\u6570\u5df2\u7ecf\u8bbe\u7f6e\u597d\u5566\uff0c\u662f\u65f6\u5019\u8fdb\u884c\u5355\u500d\u578b\u5206\u6790\u4e86\uff01<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code><span class=\"code-snippet_outer\">#Run the haplotyping at all provided epsilon values<\/span><\/code><code><span class=\"code-snippet_outer\">HapObject <- run_haplotyping(vcf = vcf,<\/span><\/code><code><span class=\"code-snippet_outer\"> LD = LD,<\/span><\/code><code><span class=\"code-snippet_outer\"> pheno = pheno,<\/span><\/code><code><span class=\"code-snippet_outer\"> metadata = metadata,<\/span><\/code><code><span class=\"code-snippet_outer\"> epsilon = epsilon,<\/span><\/code><code><span class=\"code-snippet_outer\"> MGmin = MGmin)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u5982\u679c\u4e00\u5207\u987a\u5229\uff0c\u73b0\u5728\u5df2\u7ecf\u4fdd\u5b58\u4e86\u4e00\u4e2a\u5355\u4f53\u578b\u5bf9\u8c61\uff08HapObject\uff09\uff0c\u5176\u4e2d\u5305\u542b\u4e86\u6240\u6709\u4e94\u4e2a\u63d0\u4f9b\u7684epsilon\u503c\u7684\u5355\u4f53\u578b\u7ed3\u679c\u3002\u8fd9\u4e2a\u5355\u4f53\u578b\u5bf9\u8c61\u5c06\u9700\u8981\u7528\u6765\u6784\u5efaCrossHap\u7684\u53ef\u89c6\u5316\uff08\u4ee5\u53ca\u9009\u62e9\u7684epsilon\u503c\u4ee5\u8fdb\u884c\u53ef\u89c6\u5316\uff01\uff09<\/span><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u4f18\u5316\u805a\u7c7b\u5206\u8fa8\u7387<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">Epsilon\u662fDBSCAN\u4e2d\u4e00\u4e2a\u975e\u5e38\u96be\u4ee5\u4f18\u5316\u7684\u53c2\u6570\uff0c\u8fd9\u662f\u7528\u4e8e\u5c06SNP\u805a\u7c7b\u6210CrossHap\u4e2d\u7684\u6807\u8bb0\u7ec4\uff0c\u4ee5\u8fdb\u884c\u5355\u4f53\u578b\u5206\u6790\u3002\u5e78\u8fd0\u7684\u662f\uff0ccrosshap\u6709\u4e00\u4e2aclustree\uff08Zappia\u7b49\u4eba\uff0c2018\u5e74\uff09\u5de5\u5177\uff0c\u5b83\u53ef\u4ee5\u7528\u4e8e\u603b\u7ed3\u4e0d\u540cepsilon\u503c\u4e0b\u521b\u5efa\u7684\u5355\u4f53\u578b\u5bf9\u8c61\u4e4b\u95f4\u7684\u5dee\u5f02\uff0c\u8ba9\u6211\u4eec\u53ef\u4ee5\u9009\u62e9\u6700\u4f73\u7684epsilon\u503c\u3002<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u7b2c\u4e00\u4e2a\u805a\u7c7b\u6811\u9009\u9879\u63d0\u4f9b\u4e86\u5728\u4e0d\u540cepsilon\u503c\u4e0b\u89e3\u6790\u7684\u5355\u500d\u578b\u7ec4\u7684\u53d8\u5316\u6458\u8981\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"typescript\"><code><span class=\"code-snippet_outer\">#HapObject created by `run_haplotyping`<\/span><\/code><code><span class=\"code-snippet_outer\">#Add type = 'hap' to ensure it summarizes haplotypes rather than Marker Groups<\/span><\/code><code><span class=\"code-snippet_outer\">hap_clustree <- clustree_viz(HapObject,<\/span><\/code><code><span class=\"code-snippet_outer\"> type = 'hap')<\/span><\/code><code><span class=\"code-snippet_outer\">hap_clustree<\/span><\/code><\/pre>\n<\/section>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_U4iakjc5eDY8vHXkGpZtpru38UXUtQ.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZTuqN9QZ4icc4A7AEZrDsIPLLqjU4iakjc5eDY8vHXkGpZtpru38UXUtQ\/640?wx_fmt=png'\" \/><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;text-align: left;justify-content: flex-start;\" powered-by=\"xiumi.us\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;margin-right: 4px;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 10px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;flex: 0 0 0%;height: auto;align-self: flex-end;\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\">\n<section style=\"text-align: center;transform: rotateX(180deg);\">\n<section style=\"display: inline-block;width: 3px;height: 16px;vertical-align: top;overflow: hidden;background-color: rgb(169, 207, 245);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;border-bottom: 1px solid rgb(169, 207, 245);border-bottom-right-radius: 0px;flex: 0 0 auto;align-self: flex-end;min-width: 10%;height: auto;padding: 4px 4px 4px 11px;\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h2 style=\"letter-spacing: 0.578px;white-space: normal;\"><strong><span style=\"font-size: 14px;\">\u53ef\u89c6\u5316\u5c40\u90e8\u5355\u500d\u578b<\/span><\/strong><\/h2>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<h2><span style=\"font-size: 14px;\"><\/span><\/h2>\n<p><span style=\"font-size: 14px;\">\u73b0\u5728\u6211\u4eec\u5df2\u7ecf\u5c06\u7ed3\u679c\uff08\u5355\u500d\u578b\u5bf9\u8c61\uff09\u51c6\u5907\u597d\u4e86\uff0c\u5e76\u4e14\u5df2\u7ecf\u4e3a\u6211\u4eec\u7684\u6570\u636e\u96c6\u9009\u62e9\u4e86\u6700\u4f73\u7684epsilon\u5206\u8fa8\u7387\uff0c\u662f\u65f6\u5019\u5c06\u6211\u4eec\u7684\u7ed3\u679c\u5b8c\u6574\u5730\u53ef\u89c6\u5316\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5c31\u53ef\u4ee5\u5f00\u59cb\u53d1\u73b0\u53d8\u5316\u6a21\u5f0f\u4e86!<\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u5728\u5341\u5b57\u5f62\u53ef\u89c6\u5316\u4e2d\uff0c\u4e2d\u5fc3\u77e9\u9635\u663e\u793a\u4e86\u5b9a\u4e49\u6bcf\u4e2a\u5355\u500d\u578b\u7684Marker Group\u7b49\u4f4d\u57fa\u56e0\u7684\u7ec4\u5408\uff0c\u5b83\u63d0\u4f9b\u4e86\u4e00\u4e2a\u7f51\u683c\uff0c\u56f4\u7ed5\u7740\u6bcf\u4e2aMarker Group\u548c\u5355\u500d\u578b\u7ec4\u5408\u7684\u7279\u5f81\u3002\u5355\u500d\u578b\u7684\u7279\u5f81\u548c\u5206\u914d\u7ed9\u5b83\u4eec\u7684\u4e2a\u4f53\u662f\u5782\u76f4\u53ef\u89c6\u5316\u7684\uff0c\u5728\u9876\u90e8\u548c\u5e95\u90e8\u7684\u56fe\u4e2d\u6709\u7279\u5f81\u3002\u6807\u8bb0\u7ec4\u7684\u7279\u5f81\u548c\u5206\u914d\u7ed9\u5b83\u4eec\u7684snp\u6c34\u5e73\u53ef\u89c6\u5316\uff0c\u7279\u5f81\u5728\u5de6\u8fb9\u548c\u53f3\u8fb9\u7684\u56fe\u4e0a\u3002<\/span><\/p>\n<p><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1\" data-type=\"png\" data-w=\"1080\" style=\"height: auto !important;\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ziaIoVmNapImao08hNNODOEKIqDnNA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAykBnUQkD3oVCjXDv2szbiaZLJs4kbnicdpUcemJIxQicGhsrqibziaIoVmNapImao08hNNODOEKIqDnNA\/640?wx_fmt=png'\" \/><\/p>\n<p><span style=\"font-size: 14px;\">\u8fd9\u4e9b\u56fe\u90fd\u662f\u4ec0\u4e48\u610f\u601d\uff1f<\/span><\/p>\n<ul class=\"list-paddingleft-1\">\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u5728\u4e2d\u592e\u77e9\u9635\u4e0a\u65b9\uff0c\u663e\u793a\u4e86\u6bcf\u79cd\u5355\u4f53\u578b\u7ec4\u5408\u7684\u4e2a\u4f53\u9891\u7387\uff0c\u8fd8\u6709\u6309\u6211\u4eec\u63d0\u4f9b\u7684\u5143\u6570\u636e\u53d8\u91cf\uff08\u9a6f\u5316\u7a0b\u5ea6\u6c34\u5e73\uff09\u8fdb\u884c\u7684\u5206\u89e3\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u4e0b\u65b9\uff0c\u7ed8\u5236\u4e86\u6bcf\u4e2a\u4e2a\u4f53\u7684\u8868\u578b\u5f97\u5206\uff08\u79cd\u5b50\u86cb\u767d\u8d28\u542b\u91cf\u767e\u5206\u6bd4\uff09\uff0c\u6bcf\u4e2a\u70b9\u4ee3\u8868\u4e00\u4e2a\u4e2a\u4f53\uff0c\u6839\u636e\u5355\u4f53\u578b\u5206\u7ec4\uff0c\u5e76\u6839\u636e\u5143\u6570\u636e\u53d8\u91cf\u8fdb\u884c\u7740\u8272\uff0c\u5c31\u50cf\u9876\u90e8\u7684\u6761\u5f62\u56fe\u4e00\u6837\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u5de6\u4fa7\uff0c\u662f\u6bcf\u4e2a\u6807\u8bb0\u7ec4\uff08MG\uff09\u7684\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u4fe1\u606f\u6458\u8981\u3002\u8fd9\u663e\u793a\u4e86\u6bcf\u4e2a\u6807\u8bb0\u7ec4\u5185\u6240\u6709SNP\u4e2d\u6b21\u8981\u7b49\u4f4d\u57fa\u56e0\u3001\u7f3a\u5931\u7b49\u4f4d\u57fa\u56e0\u3001\u6742\u5408\u5b50\u548c\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u7684\u9891\u7387\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u53f3\u4fa7\uff0c\u7ed8\u5236\u4e86\u6bcf\u4e2aSNP\u7684\u8868\u578b\u5173\u8054\uff08\u6bcf\u4e2a\u70b9\u4ee3\u8868\u4e00\u4e2aSNP\uff09\uff0c\u6839\u636e\u6807\u8bb0\u7ec4\u8fdb\u884c\u5206\u7ec4\u3002”\u8868\u578b\u5173\u8054” \u5b9e\u9645\u4e0a\u662f\u6307\u5bf9\u4e8e\u7ed9\u5b9a\u7684SNP\uff0c\u62e5\u6709\u66ff\u4ee3\u7b49\u4f4d\u57fa\u56e0\u548c\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u7684\u4e2a\u4f53\u4e4b\u95f4\u7684\u8868\u578b\u5f97\u5206\u5dee\u5f02\u3002<\/span><\/p>\n<\/li>\n<li style=\"font-size: 14px;\">\n<p><span style=\"font-size: 14px;\">\u53f3\u4e0b\u89d2\u7684\u8868\u683c\u603b\u7ed3\u4e86\u5355\u4f53\u578b\u4fe1\u606f\uff0c\u7684\u8868\u683c\u603b\u7ed3\u4e86\u6807\u8bb0\u7ec4\u4fe1\u606f\u3002\u6240\u6709\u7684\u56fe\u6ce8\u90fd\u663e\u793a\u5728\u5de6\u4e0b\u89d2\u3002<\/span><\/p>\n<\/li>\n<\/ul>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u7ed3\u8bed<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><span style=\"font-size: 14px;letter-spacing: 0.034em;\"><\/span><br \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"font-size: 14px;\">\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u8fd9\u4e2a\u7528\u4e8eGWAS\u7684\u5c40\u90e8\u5355\u500d\u578b\u53ef\u89c6\u5316\u7684R\u5305\uff0c\u5927\u5bb6\u4e4b\u540e\u5728\u505aGWAS\u7684\u65f6\u5019\u4e0d\u8981\u5fd8\u8bb0\u8fd9\u4e2a\u5de5\u5177\u54e6\uff01<\/span><\/p>\n<h2><span style=\"font-size: 14px;\">\u53c2\u8003\u6587\u732e<\/span><\/h2>\n<p><span style=\"font-size: 14px;\">[1] Marsh JI, Petereit J, Johnston BA, Bayer PE, Tay Fernandez CG, Al-Mamun HA, Batley J, Edwards D. crosshap: R package for local haplotype visualization for trait association analysis. Bioinformatics. 2023 Aug 1;39(8):btad518. doi: 10.1093\/bioinformatics\/btad518. PMID: 37607004; PMCID: PMC10471896.<\/span><\/p>\n<p><span style=\"font-size: 14px;\">[2] <\/span><span style=\"font-size: 14px;\">https:\/\/jacobimarsh.github.io\/crosshap\/articles\/Getting_started.html<\/span><span style=\"font-size: 14px;letter-spacing: 0.034em;\"><\/span><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" 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