MVP.Data.Hapmap2MVP: MVP.Data.Hapmap2MVP: To transform Hapmap data to MVP package...

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

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 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

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)

XiaoleiLiuBio/MVP documentation built on Sept. 27, 2024, 7:44 a.m.