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全基因组关联分析流程(三)

全基因组关联分析流程(三)

作者: 正踪大米饭儿 | 来源:发表于2018-02-28 15:24 被阅读114次

    拿到结果后,我们对结果进行展示,一般 GWAS 的标准结果图为 曼哈顿图 和 QQ 图,作图代码如下:

    ## 加载作图包
    library(qqman)
    
    ## 添加候选 SNP 标记位点显示
    candidate_Gene <- c("SYN2040", "SYN25096",
                        "SYN6161","PZE-108000718",
                        "SYN28779","PZE-108000725","SYN25098",
                        "PHM7953.11","SYN10050",
                        "SYN35436","SYN28782",
                        "SYN25094","SYN17706",
                        "PZE-109109509", "PZE-109109408",
                        "PZE-107060597", "PZE-107061311",
                        "PZE-105106278", "PZE-104065772"
                        )
    
    YN <- read.table("YN_Adjust.txt", header = T)
    
    manhattan(WJ2, main = "Manhattan Plot", 
              ylim = c(0, 10), cex = 0.6, 
              cex.axis = 0.9, 
              col = c("blue4", "orange3"), 
              suggestiveline = F, genomewideline = 4.6,
    #          chrlabs = c(1:10),
              highlight = candidate_Gene          
    )
    
    qq(WJ2$P, main = "Q-Q plot of GWAS p-values", 
       xlim = c(0, 6), ylim = c(0, 9), pch = 18, 
       col = "blue4", cex = 1.1, las = 1
      )
    
    曼哈顿图 QQ 图

    数据示例入下:


    作图数据示例

    END

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