MVP.BRENT.Vg.Ve {rMVP} | R Documentation |
MVP.BRENT.Vg.Ve variance component estimation using the BRENT method
MVP.BRENT.Vg.Ve(y, X, eigenK, verbose = FALSE)
y |
phenotype |
X |
covariate matrix, the first column is 1s |
eigenK |
eigen of Kinship matrix |
verbose |
whether to print detail. |
vg, ve, and delta
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)) eigenK <- eigen(MVP.K.VanRaden(genotype)) vc <- MVP.BRENT.Vg.Ve(y=phenotype[,2], X=matrix(1, nrow(phenotype)), eigenK=eigenK) print(vc)