MVP.Data.VCF2MVP: MVP.Data.VCF2MVP: To transform vcf data to MVP package...

In XiaoleiLiuBio/MVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

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)

XiaoleiLiuBio/MVP documentation built on April 11, 2024, 1:20 a.m.