rMVP (version 0.99.14.1)

MVP.PCA: Principal Component Analysis

Description

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

Usage

MVP.PCA(M, perc = 1, pcs.keep = 5, memo = NULL)

Arguments

M

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

perc

percentage of total SNPs selected for calculate principal components

pcs.keep

maximum number of PCs for output

memo

a marker on output file name

Value

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

Examples

# NOT RUN {
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)
str(pca)
# }