MVP.Data.Bfile2MVP: MVP.Data.Bfile2MVP: To transform plink binary data to MVP...

In rMVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

MVP.Data.Bfile2MVP: To transform plink binary data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Description

MVP.Data.Bfile2MVP: To transform plink binary data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Usage

MVP.Data.Bfile2MVP(
  bfile,
  out = "mvp",
  maxLine = 10000,
  priority = "speed",
  type.geno = "char",
  threads = 0,
  verbose = TRUE
)

Arguments

bfile	Genotype in binary format (.bed, .bim, .fam)
out	the name of output file
maxLine	the max number of line to write to big matrix for each loop
priority	'memory' or 'speed'
type.geno	the type of genotype elements
threads	number of thread for transforming
verbose	whether to print the reminder

Value

number of individuals and markers. Output files: genotype.desc, genotype.bin: genotype file in bigmemory format phenotype.phe: ordered phenotype file, same taxa order with genotype file map.map: SNP information

Examples

bfilePath <- file.path(system.file("extdata", "02_bfile", package = "rMVP"), "mvp")

MVP.Data.Bfile2MVP(bfilePath, tempfile("outfile"), threads=1)

rMVP documentation built on Nov. 27, 2023, 5:09 p.m.