MVP.Data.Numeric2MVP: MVP.Data.Numeric2MVP: To transform Numeric data to MVP...

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

MVP.Data.Numeric2MVP: To transform Numeric data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Description

MVP.Data.Numeric2MVP: To transform Numeric data to MVP package Author: Haohao Zhang Build date: Sep 12, 2018

Usage

MVP.Data.Numeric2MVP(
  num_file,
  map_file,
  out = "mvp",
  maxLine = 10000,
  row_names = FALSE,
  col_names = FALSE,
  type.geno = "char",
  auto_transpose = TRUE,
  verbose = TRUE
)

Arguments

num_file	Genotype in Numeric format (0,1,2)
map_file	Genotype map file, SNP_name, Chr, Pos
out	the name of output file
maxLine	the number of markers handled at a time, smaller value would reduce the memory cost
row_names	whether the numeric genotype has row names
col_names	whether the numeric genotype has column names
type.geno	the type of genotype elements
auto_transpose	whether to detecte the row and column
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

numericPath <- system.file("extdata", "04_numeric", "mvp.num", package = "rMVP")
mapPath <- system.file("extdata", "04_numeric", "mvp.map", package = "rMVP")
MVP.Data.Numeric2MVP(numericPath, mapPath, tempfile("outfile"))

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