使用rMVP进行gwas分析

 

001、

library(rMVP)
MVP.Data(fileBed="gwas_test",filePhe="phenotype.txt",fileKin=TRUE,filePC=TRUE,out="mvp")  ## gwas_test为plink二进制格式的文件名， phenotype.txt为表型（个体 + phe）
pheno <- read.table("mvp.phe", header = TRUE)   
head(pheno,3)
geno <- attach.big.matrix("mvp.geno.desc")    
dim(geno)
map <- read.table("mvp.geno.map", header = TRUE)   
head(map, 3)
Kinship <- attach.big.matrix("mvp.kin.desc")
dim(Kinship)
Kinship[1:5, 1:5]
Covariates <- attach.big.matrix("mvp.pc.desc")
head(Covariates)
MVP(phe=pheno,geno=geno,map=map,K=Kinship,CV.MLM=Covariates,priority="speed",      ## 运行两次？
    vc.method="EMMA",method=c("MLM"))

 

不同模型：

MVP(phe=pheno, geno=geno, map=map, maxLoop=3,
    method = "GLM", file.output= TRUE, ncpus=1)

MVP(phe=pheno, geno=geno, map=map, maxLoop=3,
           method = "MLM", file.output= TRUE, ncpus=1)

MVP(phe=pheno, geno=geno, map=map, maxLoop=3,
    method = "FarmCPU", file.output= TRUE, ncpus=1)

 

主要生成文件：