MVP.Data.PC: Principal component analysis

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

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
)

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.

Value

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

Examples

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)

XiaoleiLiuBio/MVP documentation built on Sept. 27, 2024, 7:44 a.m.