simer.Data.Bfile2MVP {simer}

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

Description

transforming plink binary data to MVP package.

Usage

simer.Data.Bfile2MVP(
  bfile,
  out = "simer",
  maxLine = 10000,
  priority = "speed",
  type.geno = "char",
  threads = 10,
  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.

Details

Build date: Sep 12, 2018 Last update: July 25, 2022

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

Author(s)

Haohao Zhang and Dong Yin

Examples

# Get bfile path
bfilePath <- file.path(system.file("extdata", "02plinkb", package = "simer"), "demo")

# Data converting
simer.Data.Bfile2MVP(bfilePath, tempfile("outfile"))