R语言实现GWAS meta分析（1）

weixin_49320263

于 2024-10-26 20:00:04 发布

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本文链接：https://blog.youkuaiyun.com/weixin_49320263/article/details/143195767

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1、基于数据集的Meta分析

datafilename=c("data1.txt","data2.txt"),
setwd(workdir)
library(Metalgwas)
a=1
name1=c()
for(i in datafilename){  assign(paste("file",a,sep=""),data.table::fread(paste(getwd(),"/","data",a,".txt",sep="")))
    name1=c(name1,paste(workdir,"//","data",a,".txt",sep=""))
    a=a+1}
METAL_gwas(GWASfile =name1, Metal_path = "XXXX",#/metal.exe : 放入下载好的软件
                    save_path = "./", GWAS_name = “dat1”, 
                    type = "outcome",Analysis_Scheme = "SE", 
                    heterogeneity = TRUE, Average_FREQ = TRUE, 
                    MinMax_FREQ = TRUE, Filter_N = FALSE, Filter_MAF = 0.01, 
                    Genomic_Control_Correction = FALSE, Sample_Overlap_Correction = FALSE)

需要下载metal：Metal - Meta Analysis Helper for SNP data

得出来结果在文件夹中dat1.txt