rMVP (version 0.99.14.1)

MVP.GEMMA.Vg.Ve: To estimate variance component using HE regression

Description

Build date: Feb 2, 2017 Last update: Feb 2, 2017

Usage

MVP.GEMMA.Vg.Ve(y, X, K, rtol = 1e-06, atol = 1e-08, ctol = 1e-08)

Arguments

y

phenotype

X

genotype

K

kinship matrix

rtol

parameters for HE regression, no changes is recommended

atol

parameters for HE regression, no changes is recommended

ctol

parameters for HE regression, no changes is recommended

Value

vg, ve, and delta

Examples

# NOT RUN {
phePath <- system.file("extdata", "07_other", "mvp.phe", package = "rMVP")
phenotype <- read.table(phePath, header=TRUE)
print(dim(phenotype))
genoPath <- system.file("extdata", "06_mvp-impute", "mvp.imp.geno.desc", package = "rMVP")
genotype <- attach.big.matrix(genoPath)
print(dim(genotype))
K <- MVP.K.VanRaden(genotype)
vc <- MVP.GEMMA.Vg.Ve(y=phenotype[,2], X=matrix(1, nrow(phenotype)), K=K)
print(vc)
# }