rMVP (version 1.1.1)

MVP.Data.PC: Principal component analysis

Description

Principal component analysis

Usage

MVP.Data.PC(
  filePC = TRUE,
  mvp_prefix = "mvp",
  K = NULL,
  out = NULL,
  pcs.keep = 5,
  maxLine = 10000,
  sep = "\t",
  cpu = 1,
  verbose = TRUE
)

Value

Output file: <out>.pc.bin <out>.pc.desc

Arguments

filePC

Principal components, n*npc, n is sample size, npc is number of top columns of principal components

mvp_prefix

Prefix for mvp format files

K

Kinship matrix

out

prefix of output file name

pcs.keep

how many PCs to keep

maxLine

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

sep

seperator for PC file.

cpu

the number of cpu

verbose

whether to print detail.

Examples

# \donttest{
geno <- file.path(system.file("extdata", "06_mvp-impute", package = "rMVP"), "mvp.imp")

MVP.Data.PC(TRUE, mvp_prefix=geno, out=tempfile("outfile"), cpu=1)
# }