rMVP (version 1.1.1)

MVP.Data.VCF2MVP: 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
)

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

Arguments

vcf_file

Genotype in VCF format

out

the name of output file

maxLine

the number of markers handled at a time, smaller value would reduce the memory cost

type.geno

the type of genotype elements

threads

number of thread for transforming

verbose

whether to print the reminder

Examples

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

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