MVP.Data.VCF2MVP {rMVP}

MVP.Data.VCF2MVP: To transform vcf data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Description

Accept the | or / separated markers, any variant sites that are not 0 or 1 will be considered NA.

Usage

MVP.Data.VCF2MVP(
  vcf_file,
  out = "mvp",
  maxLine = 10000,
  type.geno = "char",
  threads = 1,
  verbose = TRUE
)

Arguments

vcf_file

Genotype in VCF 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

vcfPath <- system.file("extdata", "01_vcf", "mvp.vcf", package = "rMVP")

MVP.Data.VCF2MVP(vcfPath, tempfile("outfile"), threads=1)