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: