"use strict"; const {Fragment: _Fragment, jsx: _jsx, jsxs: _jsxs} = arguments[0]; const {useMDXComponents: _provideComponents} = arguments[0]; function _createMdxContent(props) { const _components = { a: "a", code: "code", div: "div", h2: "h2", h3: "h3", h4: "h4", h5: "h5", img: "img", p: "p", path: "path", pre: "pre", span: "span", strong: "strong", svg: "svg", ..._provideComponents(), ...props.components }; return _jsxs(_Fragment, { children: [_jsxs(_components.h2, { id: "一-基本用法", children: [_jsx(_components.a, { className: "heading-link", href: "#一-基本用法", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "一、基本用法"] }), "\n", _jsxs(_components.h3, { id: "01-assoc", children: [_jsx(_components.a, { className: "heading-link", href: "#01-assoc", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "01 assoc"] }), "\n", _jsx(_components.p, { children: "基本的case/control关联，质量性状数量性状均可，不能加协变量" }), "\n", _jsxs(_components.h4, { id: "数据过滤", children: [_jsx(_components.a, { className: "heading-link", href: "#数据过滤", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "数据过滤"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " /stor9000/apps/users/NWSUAF/2020060179/Sheep/GWAS/all_sample339.snp.filtered2.final.rename.modified --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--recode" }), " transpose ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--maf" }), " ", _jsx(_components.span, { className: "token number", children: "0.05" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--geno" }), " ", _jsx(_components.span, { className: "token number", children: "0.1" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--mind" }), " ", _jsx(_components.span, { className: "token number", children: "0.1" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--hwe" }), " ", _jsx(_components.span, { className: "token number", children: "0.001" }), " --autosome-xy --allow-extra-chr\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) }), "\n", _jsxs(_components.h4, { id: "整理性状", children: [_jsx(_components.a, { className: "heading-link", href: "#整理性状", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "整理性状"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token function", children: "cut" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-d" }), " ", _jsx(_components.span, { className: "token string", children: "\" \"" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-f" }), " ", _jsx(_components.span, { className: "token number", children: "1" }), " all_sample339.snp.filtered2.final.rename.modified323.filter.tfam ", _jsx(_components.span, { className: "token operator", children: ">" }), " samples\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "for" }), " ", _jsx(_components.span, { className: "token for-or-select variable", children: "i" }), " ", _jsx(_components.span, { className: "token keyword", children: "in" }), " ", _jsxs(_components.span, { className: "token variable", children: [_jsx(_components.span, { className: "token variable", children: "`" }), _jsx(_components.span, { className: "token function", children: "cat" }), " samples", _jsx(_components.span, { className: "token variable", children: "`" })] }), _jsx(_components.span, { className: "token punctuation", children: ";" }), " ", _jsx(_components.span, { className: "token keyword", children: "do" }), " ", _jsx(_components.span, { className: "token function", children: "grep" }), " ", _jsx(_components.span, { className: "token variable", children: "$i" }), " /stor9000/apps/users/NWSUAF/2020060179/Sheep/GWAS/trait_tail_type2 ", _jsx(_components.span, { className: "token operator", children: ">>" }), " tail_wool", _jsx(_components.span, { className: "token punctuation", children: ";" }), _jsx(_components.span, { className: "token keyword", children: "done" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token function", children: "sed" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-i" }), " ", _jsx(_components.span, { className: "token string", children: "'s/1$/2/g'" }), " tail_wool\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token function", children: "sed" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-i" }), " ", _jsx(_components.span, { className: "token string", children: "'s/0$/1/g'" }), " tail_wool\n"] })] }) }), "\n", _jsxs(_components.h4, { id: "关联分析", children: [_jsx(_components.a, { className: "heading-link", href: "#关联分析", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "关联分析"] }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "# 质量性状，默认基于卡方检验，\n" }), _jsx(_components.span, { className: "code-line", children: "plink --tfile ../all_sample339.snp.filtered2.final.rename.modified323.filter --pheno tail_wool --assoc --out tail_wool.assoc --chr-set 26 --allow-no-sex\n" }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) }), "\n", _jsxs(_components.div, { "data-callout": true, "data-callout-type": "info", children: ["\n", _jsx(_components.div, { "data-callout-title": true, children: "Info" }), "\n", _jsxs(_components.div, { "data-callout-body": true, children: ["\n", _jsx(_components.p, { children: "也可以加–fisher进行Fisher精确检验计算精确P值，否则–assoc默认根据chi square分布计算近似P值。\n在大样本的情况下（总样本数＞40），可以用chi square检验，若总样本数＜40，单个最小频数＜5，则用fisher检验较为合适。" }), "\n"] }), "\n"] }), "\n", _jsx(_components.p, { children: "结果文件格式：" }), "\n", _jsxs(_components.p, { children: [_jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410110908477.png", alt: "image.png", className: "internal" }), "\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410110938665.png", alt: "image.png", className: "internal" })] }), "\n", _jsxs(_components.div, { "data-callout": true, "data-callout-type": "info", children: ["\n", _jsx(_components.div, { "data-callout-title": true, children: "Info" }), "\n", _jsxs(_components.div, { "data-callout-body": true, children: ["\n", _jsxs(_components.p, { children: ["对于数量性状，基于t检验，", _jsx(_components.strong, { children: "对于数量性状来说–assoc结果和–linear以及–logistic中的ADD效应的P值一样" }), "："] }), "\n"] }), "\n"] }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "# \n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "plink --tfile ../all_sample339.snp.filtered2.final.rename.modified323.filter --pheno tail_length --assoc --out tail_length.assoc --chr-set 26 --allow-no-sex\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "# 结果文件格式\n" }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) }), "\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410110940526.png", alt: "image.png", className: "internal" }), "\n", _jsxs(_components.div, { "data-callout": true, "data-callout-type": "warning", children: ["\n", _jsx(_components.div, { "data-callout-title": true, children: "Warning" }), "\n", _jsxs(_components.div, { "data-callout-body": true, children: ["\n", _jsx(_components.p, { children: "协变量为分类变量时，需要转换为虚拟变量/哑变量" }), "\n"] }), "\n"] }), "\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410110941985.png", alt: "image.png", className: "internal" }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsx(_components.code, { className: "language-shell code-highlight", children: _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/covariate_for_plink --write-covar --dummy-coding ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/dummy_covariate_for_plink --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), "\n"] }) }) }), "\n", _jsxs(_components.h3, { id: "02-logistic", children: [_jsx(_components.a, { className: "heading-link", href: "#02-logistic", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "02 logistic"] }), "\n", _jsx(_components.p, { children: "**逻辑回归，用于分类变量，可以添加协变量，基于t检验" }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# PCA结果作为协变量" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--pca" }), " --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--maf" }), " ", _jsx(_components.span, { className: "token number", children: "0.05" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " all_sample339.snp.filtered2.final.rename.modified323.filter.pca\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 关联" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " tail_wool ", _jsx(_components.span, { className: "token parameter variable", children: "--logistic" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/covariate_for_plink ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " tail_wool.logistic --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " --allow-no-sex\n"] })] }) }), "\n", _jsxs(_components.h3, { id: "03-linear", children: [_jsx(_components.a, { className: "heading-link", href: "#03-linear", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "03 linear"] }), "\n", _jsx(_components.p, { children: "线性回归，用于连续性变量，可以添加协变量，基于t检验" }), "\n", _jsxs(_components.h4, { id: "不加协变量", children: [_jsx(_components.a, { className: "heading-link", href: "#不加协变量", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "不加协变量"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsx(_components.code, { className: "language-shell code-highlight", children: _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " tail_length ", _jsx(_components.span, { className: "token parameter variable", children: "--linear" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " tail_length.linear.nocov --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " --allow-no-sex\n"] }) }) }), "\n", _jsxs(_components.h4, { id: "加协变量", children: [_jsx(_components.a, { className: "heading-link", href: "#加协变量", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "加协变量"] }), "\n", _jsxs(_components.p, { children: ["协变量格式:\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410111033866.png", alt: "image.png", className: "internal" })] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 关联" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/all_sample339.snp.filtered2.final.rename.modified323.filter ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " tail_length ", _jsx(_components.span, { className: "token parameter variable", children: "--linear" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/covariate_for_plink ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " tail_length.linear --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " --allow-no-sex\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 可以加上--hide-covar参数，不显示协变量，只显示ADD加性效应。" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/all_sample339.snp.filtered2.final.rename.modified323.filter --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/all_phenotypes --pheno-name Birth_weight ", _jsx(_components.span, { className: "token parameter variable", children: "--linear" }), " --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " birth_weight.linear.cov1 ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/covariate_for_plink --hide-covar\n"] })] }) }), "\n", _jsxs(_components.h2, { id: "二进阶技巧", children: [_jsx(_components.a, { className: "heading-link", href: "#二进阶技巧", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "二、进阶技巧"] }), "\n", _jsxs(_components.h3, { id: "01-所有表型一起做", children: [_jsx(_components.a, { className: "heading-link", href: "#01-所有表型一起做", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "01 所有表型一起做"] }), "\n", _jsxs(_components.p, { children: ["表型文件格式：\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410111035245.png", alt: "image.png", className: "internal" })] }), "\n", _jsxs(_components.div, { "data-callout": true, "data-callout-type": "warning", children: ["\n", _jsx(_components.div, { "data-callout-title": true, children: "Warning" }), "\n", _jsxs(_components.div, { "data-callout-body": true, children: ["\n", _jsx(_components.p, { children: "表型中如果用01编码二元分类性状，需要改成其它数字编码" }), "\n"] }), "\n"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 关联分析" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--assoc" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " all_phenotypes --all-pheno --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " allpheno\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# 所有表型一起做一般线性模型" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--bfile" }), " /stor9000/apps/users/NWSUAF/2015010726/Sheep/GWAS_for_HuSheep/02.GWAS/by_GEMMA/all_samples317.filter.sort --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--linear" }), " hide-covar ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " /stor9000/apps/users/NWSUAF/2015010726/Sheep/GWAS_for_HuSheep/02.GWAS/all_phenotypes.txt --all-pheno --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " allpheno ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " covariate_for_plink_pca3_age_sib\n"] })] }) }), "\n", _jsxs(_components.h3, { id: "02-当有p值为0时设定最小p值", children: [_jsx(_components.a, { className: "heading-link", href: "#02-当有p值为0时设定最小p值", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "02 当有P值为0时，设定最小P值"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# --output-min-p 1e-99 # any p-value below 10^{-99} will be reported as 10^{-99}" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--file" }), " /stor9000/apps/users/NWSUAF/2015010726/Sheep/GWAS_for_Black_Suffolk/01.data/plink/Black_Suffolk.snp.filtered ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " /stor9000/apps/users/NWSUAF/2015010726/Sheep/GWAS_for_Black_Suffolk/02.GWAS/all_pheno_mod.grep --pheno-name Chest_width ", _jsx(_components.span, { className: "token parameter variable", children: "--linear" }), " hide-covar ", _jsx(_components.span, { className: "token parameter variable", children: "--covar" }), " ", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/", _jsx(_components.span, { className: "token punctuation", children: ".." }), "/covariates_pca3 --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " Chest_width --output-min-p 1e-99\n"] })] }) }), "\n", _jsxs(_components.h3, { id: "03-加上多重检验的关联分析", children: [_jsx(_components.a, { className: "heading-link", href: "#03-加上多重检验的关联分析", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "03 加上多重检验的关联分析"] }), "\n", _jsxs(_components.h4, { id: "bonferroni校正", children: [_jsx(_components.a, { className: "heading-link", href: "#bonferroni校正", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "Bonferroni校正"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsx(_components.code, { className: "language-shell code-highlight", children: _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--assoc" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " all_phenotypes --pheno-name tail_type --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " ", _jsx(_components.span, { className: "token builtin class-name", children: "type" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--adjust" }), "\n"] }) }) }), "\n", _jsxs(_components.p, { children: ["结果文件格式：\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410111126747.png", alt: "image.png", className: "internal" })] }), "\n", _jsxs(_components.h4, { id: "permutation校正", children: [_jsx(_components.a, { className: "heading-link", href: "#permutation校正", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "permutation校正"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsxs(_components.code, { className: "language-shell code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--assoc" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " all_phenotypes --pheno-name tail_type --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " ", _jsx(_components.span, { className: "token builtin class-name", children: "type" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--mperm" }), " ", _jsx(_components.span, { className: "token number", children: "10000" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# or" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["plink ", _jsx(_components.span, { className: "token parameter variable", children: "--tfile" }), " all_sample339.snp.filtered2.final.rename.modified323.filter --chr-set ", _jsx(_components.span, { className: "token number", children: "26" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--assoc" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "--pheno" }), " all_phenotypes --pheno-name Tail_length --allow-no-sex ", _jsx(_components.span, { className: "token parameter variable", children: "--out" }), " Tail_length_msperm ", _jsx(_components.span, { className: "token parameter variable", children: "--mperm" }), " ", _jsx(_components.span, { className: "token number", children: "10000" }), "\n"] })] }) }), "\n", _jsxs(_components.h5, { id: "结果文件", children: [_jsx(_components.a, { className: "heading-link", href: "#结果文件", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "结果文件"] }), "\n", _jsx(_components.p, { children: "sort -k4,4 -g Tail_length_msperm.qassoc.mperm | head" }), "\n", _jsx(_components.img, { src: "https://picbed.guoyingwei.top/2024/10/202410111127223.png", alt: "image.png", className: "internal" }), "\n", _jsxs(_components.h2, { id: "三可视化与注释", children: [_jsx(_components.a, { className: "heading-link", href: "#三可视化与注释", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "三、可视化与注释"] }), "\n", _jsxs(_components.h3, { id: "01-可视化曼哈顿图", children: [_jsx(_components.a, { className: "heading-link", href: "#01-可视化曼哈顿图", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "01 可视化曼哈顿图"] }), "\n", _jsxs(_components.h4, { id: "提取p值", children: [_jsx(_components.a, { className: "heading-link", href: "#提取p值", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "提取P值"] }), "\n", _jsx(_components.pre, { className: "language-shell", children: _jsx(_components.code, { className: "language-shell code-highlight", children: _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token function", children: "awk" }), " ", _jsx(_components.span, { className: "token string", children: "'{OFS=\"\\t\"}{print $1,$3,$9}'" }), " tail_length.linear.nocov.assoc.linear ", _jsx(_components.span, { className: "token operator", children: "|" }), " ", _jsx(_components.span, { className: "token function", children: "grep" }), " ", _jsx(_components.span, { className: "token parameter variable", children: "-v" }), " ", _jsx(_components.span, { className: "token string", children: "'NA'" }), " ", _jsx(_components.span, { className: "token operator", children: ">" }), " tail_length.linear.nocov.assoc.linear.pvalue.txt\n"] }) }) }), "\n", _jsxs(_components.h4, { id: "可视化", children: [_jsx(_components.a, { className: "heading-link", href: "#可视化", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "可视化"] }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "##可视化\n" }), _jsx(_components.span, { className: "code-line", children: "library(qqman)\n" }), _jsx(_components.span, { className: "code-line", children: "data <- read.table(\"C:/Users/Administrator/Desktop/gwas.assoc.txt\",header = T) # 读取数去存到data变量里面\n" }), _jsx(_components.span, { className: "code-line", children: "colorset<-c(\"blue4\", \"orange3\") # 创建一个颜色集合\n" }), _jsx(_components.span, { className: "code-line", children: "manhattan(data, CHR = \"CHR\", BP = \"bp\", SNP = \"SNP\", p = \"P-VALUE\", col = colorset) # 画曼哈顿图\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "# 或者服务器上一键式\n" }), _jsx(_components.span, { className: "code-line", children: "source /stor9000/apps/users/NWSUAF/2015010726/.bashrc\n" }), _jsx(_components.span, { className: "code-line", children: "export R_LIBS_USER=\"/stor9000/apps/users/NWSUAF/2015010726/R/x86_64-conda_cos6-linux-gnu-library/3.5/\"\n" })] }) }), "\n", _jsxs(_components.h4, { id: "r脚本内容", children: [_jsx(_components.a, { className: "heading-link", href: "#r脚本内容", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "R脚本内容"] }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "############################ /stor9000/apps/users/NWSUAF/2015010726/scripts/Manhattan_QQ_plot.R脚本内容#################################\n" }), _jsx(_components.span, { className: "code-line", children: "# Object: Manhattan & QQ Plot for genome-wide association study\n" }), _jsx(_components.span, { className: "code-line", children: "# Output: Single figure with PDF format\n" }), _jsx(_components.span, { className: "code-line", children: "# Authors: Yingwei Guo\n" }), _jsx(_components.span, { className: "code-line", children: "# Date: 8th, Jan, 2021\n" }), _jsx(_components.span, { className: "code-line", children: "# Usage: Rscript commandArgs()[4] pvalue.txt sites_number traits_name\n" }), _jsx(_components.span, { className: "code-line", children: "# 如果报没有qqman这个包的错误，在shell环境运行下面一行命令：\n" }), _jsx(_components.span, { className: "code-line", children: "# export R_LIBS_USER=\"/stor9000/apps/users/NWSUAF/2015010726/R/x86_64-conda_cos6-linux-gnu-library/3.5/\"\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "library(qqman)\n" }), _jsx(_components.span, { className: "code-line", children: "args <- commandArgs(trailingOnly = TRUE)\n" }), _jsx(_components.span, { className: "code-line", children: "data <- read.table(args[1],header = T) # 读取数去存到data变量里面\n" }), _jsx(_components.span, { className: "code-line", children: "colorset <- c(\"#4C72B0\", \"#DD8452\") # 创建一个颜色集合\n" }), _jsx(_components.span, { className: "code-line", children: "pdf(paste0(args[3], \".pdf\"), width = 18,height=4.5)\n" }), _jsx(_components.span, { className: "code-line", children: "layout(matrix(c(1,2), 1, 2, byrow = TRUE),widths=c(3,1), heights=c(1,1))\n" }), _jsx(_components.span, { className: "code-line", children: "par(mar = (c(3,4,2,2)+ 0.5), mgp=c(1.6,1,0))\n" }), _jsx(_components.span, { className: "code-line", children: "par(bty=\"l\", lwd=1.5) ## bty=l the plot is coordinate instead of box\n" }), _jsx(_components.span, { className: "code-line", children: "manhattan(data, CHR = \"CHR\", BP = \"BP\", SNP=\"SNP\", p = \"P\", suggestiveline = F, genomewideline = F, cex = 0.8) # 画曼哈顿图，默认是黑色和灰色，加color=colorset可自定义\n" }), _jsx(_components.span, { className: "code-line", children: "sites_number <- as.numeric(args[2])\n" }), _jsx(_components.span, { className: "code-line", children: "abline(h=-log10(0.05/sites_number), lty=5, col=\"grey40\") # 自定义阈值线，h=-log10(0.05/sites_number)\n" }), _jsx(_components.span, { className: "code-line", children: "qq(data$P, cex = 0.8)\n" }), _jsx(_components.span, { className: "code-line", children: "dev.off()\n" }), _jsx(_components.span, { className: "code-line", children: "#############################################################################################################################\n" })] }) }), "\n", _jsxs(_components.h4, { id: "用法", children: [_jsx(_components.a, { className: "heading-link", href: "#用法", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "用法"] }), "\n", _jsx(_components.pre, { children: _jsxs(_components.code, { className: "language-auto code-highlight", children: [_jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "Rscript /stor9000/apps/users/NWSUAF/2015010726/scripts/Manhattan_QQ_plot.R P值列不包含NA的GWAS结果文件位点数性状名字\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "例如：\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "Rscript /stor9000/apps/users/NWSUAF/2015010726/scripts/Manhattan_QQ_plot.R Birth_weight.pvalue.txt 281613 Birth_weight.mht\n" }), _jsx(_components.span, { className: "code-line", children: "\n" })] }) }), "\n", _jsxs(_components.h3, { id: "02-位点过多时的可视化方式感谢好朋友提醒", children: [_jsx(_components.a, { className: "heading-link", href: "#02-位点过多时的可视化方式感谢好朋友提醒", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "02 位点过多时的可视化方式（感谢好朋友提醒）"] }), "\n", _jsx(_components.p, { children: "可视化的本质是把每个点以pos为横坐标，以P值为纵坐标标注在坐标轴上。因此，当位点数目超过百万级别时，生成速度很慢，可以用下面的脚本进行可视化。原理大概是，把那些P值不显著有距离相近的位点去除一些，这样在图上显示看起来是一样的。" }), "\n", _jsx(_components.p, { children: "脚本中定义了一个名为 GAPIT.Pruning 的函数，该函数的主要目的是从大量数据点中筛选出一个子集，以便在绘图时只展示这些代表性点，从而减少绘图的复杂度和时间。" }), "\n", _jsxs(_components.h4, { id: "优化后的脚本", children: [_jsx(_components.a, { className: "heading-link", href: "#优化后的脚本", children: _jsx(_components.svg, { xmlns: "http:www.w3.org/2000/svg", fill: "#ab2b65", viewBox: "0 0 20 20", className: "w-5 h-5", children: _jsx(_components.path, { fillRule: "evenodd", clipRule: "evenodd", d: "M9.493 2.853a.75.75 0 00-1.486-.205L7.545 6H4.198a.75.75 0 000 1.5h3.14l-.69 5H3.302a.75.75 0 000 1.5h3.14l-.435 3.148a.75.75 0 001.486.205L7.955 14h2.986l-.434 3.148a.75.75 0 001.486.205L12.456 14h3.346a.75.75 0 000-1.5h-3.14l.69-5h3.346a.75.75 0 000-1.5h-3.14l.435-3.147a.75.75 0 00-1.486-.205L12.045 6H9.059l.434-3.147zM8.852 7.5l-.69 5h2.986l.69-5H8.852z" }) }) }), "优化后的脚本"] }), "\n", _jsx(_components.pre, { className: "language-r", children: _jsxs(_components.code, { className: "language-R code-highlight", children: [_jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "##########################################MANHATTAN_QQ.r#######################################" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Object: Manhattan & QQ Plot for genome-wide association study" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Output: Single figure with PDF format" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Authors: Zhiwu Zhang" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Modified by Zhengkui Zhou (zkzhou@126.com) " }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "# Last update: Feb 8, 2014" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["`GAPIT.Pruning` ", _jsx(_components.span, { className: "token operator", children: "<-" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "function" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: "," }), "DPP", _jsx(_components.span, { className: "token operator", children: "=" }), _jsx(_components.span, { className: "token number", children: "5000" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "{" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token keyword", children: "if" }), _jsx(_components.span, { className: "token punctuation", children: "(" }), "length", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token operator", children: "<=" }), "DPP", _jsx(_components.span, { className: "token punctuation", children: ")" }), "return", _jsx(_components.span, { className: "token punctuation", children: "(" }), "c", _jsx(_components.span, { className: "token punctuation", children: "(" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token operator", children: ":" }), "length", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: " \n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#values= log.P.values" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["values", _jsx(_components.span, { className: "token operator", children: "=" }), "sqrt", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), " ", _jsx(_components.span, { className: "token comment", children: "#This shift the weight a little bit to the low building." }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token comment", children: "#Handler of bias plot" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["rv", _jsx(_components.span, { className: "token operator", children: "=" }), "runif", _jsx(_components.span, { className: "token punctuation", children: "(" }), "length", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["values", _jsx(_components.span, { className: "token operator", children: "=" }), "values", _jsx(_components.span, { className: "token operator", children: "+" }), "rv\n"] }), _jsxs(_components.span, { className: "code-line", children: ["values", _jsx(_components.span, { className: "token operator", children: "=" }), "values", _jsx(_components.span, { className: "token punctuation", children: "[" }), "order", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: "," }), "decreasing ", _jsx(_components.span, { className: "token operator", children: "=" }), " T", _jsx(_components.span, { className: "token punctuation", children: ")" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["theMin", _jsx(_components.span, { className: "token operator", children: "=" }), "min", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["theMax", _jsx(_components.span, { className: "token operator", children: "=" }), "max", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["range", _jsx(_components.span, { className: "token operator", children: "=" }), "theMax", _jsx(_components.span, { className: "token operator", children: "-" }), "theMin\n"] }), _jsxs(_components.span, { className: "code-line", children: ["interval", _jsx(_components.span, { className: "token operator", children: "=" }), "range", _jsx(_components.span, { className: "token operator", children: "/" }), "DPP\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["ladder", _jsx(_components.span, { className: "token operator", children: "=" }), "round", _jsx(_components.span, { className: "token punctuation", children: "(" }), "values", _jsx(_components.span, { className: "token operator", children: "/" }), "interval", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["ladder2", _jsx(_components.span, { className: "token operator", children: "=" }), "c", _jsx(_components.span, { className: "token punctuation", children: "(" }), "ladder", _jsx(_components.span, { className: "token punctuation", children: "[" }), _jsx(_components.span, { className: "token operator", children: "-" }), _jsx(_components.span, { className: "token number", children: "1" }), _jsx(_components.span, { className: "token punctuation", children: "]" }), _jsx(_components.span, { className: "token punctuation", children: "," }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: ["keep", _jsx(_components.span, { className: "token operator", children: "=" }), "ladder", _jsx(_components.span, { className: "token operator", children: "-" }), "ladder2\n"] }), _jsxs(_components.span, { className: "code-line", children: ["index", _jsx(_components.span, { className: "token operator", children: "=" }), "which", _jsx(_components.span, { className: "token punctuation", children: "(" }), "keep", _jsx(_components.span, { className: "token operator", children: ">" }), _jsx(_components.span, { className: "token number", children: "0" }), _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsx(_components.span, { className: "code-line", children: "\n" }), _jsxs(_components.span, { className: "code-line", children: ["return", _jsx(_components.span, { className: "token punctuation", children: "(" }), "index", _jsx(_components.span, { className: "token punctuation", children: ")" }), "\n"] }), _jsxs(_components.span, { className: "code-line", children: [_jsx(_components.span, { className: "token punctuation", children: "}" }), _jsx(_components.span, { 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