rMVP (version 0.99.14.1)

MVP.Data.QC: MVP.Data.QC: quality control of genotype Author: Haohao Zhang Build date: Sep 12, 2018

Description

MVP.Data.QC: quality control of genotype Author: Haohao Zhang Build date: Sep 12, 2018

Usage

MVP.Data.QC(mvp_prefix, out = NULL, geno = 0.1, mind = 0.1,
  maf = 0.05, hwe = NULL, ncpus = NULL)

Arguments

mvp_prefix

the prefix of genotype file

out

the prefix of output file

geno

the threshold of calling rate of markers

mind

the threshold of calling rate of individuals

maf

the threshold of minor allel frequency

hwe

the threshold of hwe

ncpus

the number of threads for quality control

Value

NULL Output files: cleaned genotype file

Examples

# NOT RUN {
geno <- file.path(system.file("extdata", "05_mvp", package = "rMVP"), "mvp")
MVP.Data.QC(geno, out="rMVP.test.qc", ncpus=1)
# }