Error in analysing the all phenotype

[ramendra-sarma]

I am geting GWAS result for one penotype, not for all with the given rodes. How to get analysis of all phenotypic data? Please suggest.

library(rMVP)
MVP.Data(fileVCF="reheader.vcf",
filePhe="mcv_pheno_N.csv",
fileKin=FALSE,
filePC=FALSE,
out="mvp.vcf"
)
map_info <- read.table("mvp.vcf.geno.map" , head = TRUE)
genotypic_dat <- attach.big.matrix("mvp.vcf.geno.desc")
phenotype_dat <- read.table("mvp.vcf.phe",head=TRUE)
print(dim(phenotype))
GWAS_PCA_mvp <- MVP(
phe = phenotype_dat,
geno = genotypic_dat,
map = map_info,
method = c("GLM", "MLM", "FarmCPU"),
nPC.GLM = 5,file.output=TRUE,
nPC.MLM = 5,
nPC.FarmCPU = 5,
)