MVP.Data.Hapmap2MVP {rMVP}

MVP.Data.Hapmap2MVP: To transform Hapmap data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Description

MVP.Data.Hapmap2MVP: To transform Hapmap data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Usage

MVP.Data.Hapmap2MVP(
  hmp_file,
  out = "mvp",
  maxLine = 10000,
  type.geno = "char",
  threads = 1,
  verbose = TRUE
)

Arguments

hmp_file

Genotype in Hapmap format

out

the name of output file

maxLine

the max number of line to write to big matrix for each loop

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

hapmapPath <- system.file("extdata", "03_hapmap", "mvp.hmp.txt", package = "rMVP")

MVP.Data.Hapmap2MVP(hapmapPath, tempfile("outfile"), threads=1)