rMVP (version 1.1.1)

MVP.K.VanRaden: Calculate Kinship matrix by VanRaden method

Description

Build date: Dec 12, 2016 Last update: Dec 12, 2019

Usage

MVP.K.VanRaden(
  M,
  maxLine = 5000,
  ind_idx = NULL,
  cpu = 1,
  verbose = TRUE,
  checkNA = TRUE
)

Value

K, n * n matrix

Arguments

M

Genotype, m * n, m is marker size, n is population size

maxLine

the number of markers handled at a time, smaller value would reduce the memory cost

ind_idx

the index of effective genotyped individuals used in analysis

cpu

the number of cpu

verbose

whether to print detail.

checkNA

whether to check NA in genotype.

Examples

# \donttest{
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, cpu=1)
# }