MVP.PCA {rMVP}

Principal Component Analysis

Description

Build date: Dec 14, 2016 Last update: Oct 29, 2018

Usage

MVP.PCA(
  M = NULL,
  K = NULL,
  priority = c("speed", "memory"),
  pcs.keep = 5,
  cpu = 1,
  verbose = TRUE
)

Arguments

M

Genotype in numeric format, pure 0, 1, 2 matrix; m * n, m is marker size, n is population size

K

kinship matrix

priority

speed or memory

pcs.keep

maximum number of PCs for output

cpu

the number of cpu

verbose

whether to print detail.

Value

Output: PCs - a n * npc matrix of top number of PCs, n is population size and npc is @param pcs.keep

Author(s)

Xiaolei Liu, Lilin Yin and Haohao Zhang

Examples

genoPath <- system.file("extdata", "06_mvp-impute", "mvp.imp.geno.desc", package = "rMVP")
genotype <- attach.big.matrix(genoPath)
print(dim(genotype))

pca <- MVP.PCA(M=genotype, cpu=1)
str(pca)