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

In XiaoleiLiuBio/MVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

Calculate Kinship matrix by VanRaden method

Description

Calculate Kinship matrix by VanRaden method

Usage

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

Arguments

M	genotype, either m by n or n by m is supportable, 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
mrk_idx	the index of effective markers used in analysis
mrk_freq	the prior calculated major allele frequency (not MAF) for all markers used in analysis
mrk_bycol	whether the markers are stored by columns in genotype (i.e. M is a n by m matrix)
cpu	the number of cpu
verbose	whether to print detail.
checkNA	whether to check NA in genotype.

Value

K, n * n matrix

Examples

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)

XiaoleiLiuBio/MVP documentation built on Jan. 3, 2025, 5:59 a.m.