MVP.Data: MVP.Data: To prepare data for MVP package Author: Xiaolei...

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

MVP.Data: To prepare data for MVP package Author: Xiaolei Liu, Lilin Yin and Haohao Zhang Build date: Aug 30, 2016 Last update: Sep 12, 2018

Description

MVP.Data: To prepare data for MVP package Author: Xiaolei Liu, Lilin Yin and Haohao Zhang Build date: Aug 30, 2016 Last update: Sep 12, 2018

Usage

MVP.Data(
  fileMVP = NULL,
  fileVCF = NULL,
  fileHMP = NULL,
  fileBed = NULL,
  fileNum = NULL,
  fileMap = NULL,
  filePhe = NULL,
  fileInd = NULL,
  fileKin = NULL,
  filePC = NULL,
  out = "mvp",
  sep.num = "\t",
  auto_transpose = TRUE,
  sep.map = "\t",
  sep.phe = "\t",
  sep.kin = "\t",
  sep.pc = "\t",
  type.geno = "char",
  pheno_cols = NULL,
  SNP.impute = "Major",
  maxLine = 10000,
  pcs.keep = 5,
  verbose = TRUE,
  ncpus = NULL,
  ...
)

Arguments

fileMVP	Genotype in MVP format
fileVCF	Genotype in VCF format
fileHMP	Genotype in hapmap format
fileBed	Genotype in PLINK binary format
fileNum	Genotype in numeric format; pure 0, 1, 2 matrix; m * n, m is marker size, n is sample size
fileMap	SNP map information, there are three columns, including SNP_ID, Chromosome, and Position
filePhe	Phenotype, the first column is taxa name, the subsequent columns are traits
fileInd	Individual name file
fileKin	Kinship that represents relationship among individuals, n * n matrix, n is sample size
filePC	Principal components, n*npc, n is sample size, npc is number of top columns of principal components
out	prefix of output file name
sep.num	seperator for numeric file.
auto_transpose	Whether to automatically transpose numeric genotypes, the default is True, which will identify the most one of the rows or columns as a marker, If set to False, the row represents the marker and the column represents the individual.
sep.map	seperator for map file.
sep.phe	seperator for phenotype file.
sep.kin	seperator for Kinship file.
sep.pc	seperator for PC file.
type.geno	type parameter in bigmemory, genotype data. The default is char, it is highly recommended *NOT* to modify this parameter.
pheno_cols	Extract which columns of the phenotype file (including individual IDs)
SNP.impute	"Left", "Middle", "Right", or NULL for skip impute.
maxLine	the number of markers handled at a time, smaller value would reduce the memory cost
pcs.keep	how many PCs to keep
verbose	whether to print detail.
ncpus	The number of threads used, if NULL, (logical core number - 1) is automatically used
...	Compatible with DEPRECATED parameters.

Value

NULL 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 k.desc, k.bin: Kinship matrix in bigmemory format pc.desc, pc.bin: PC matrix in bigmemory format Requirement: fileHMP, fileBed, and fileNum can not input at the same time

Examples

bfilePath <- file.path(system.file("extdata", "02_bfile", package = "rMVP"), "mvp")
opts <- options(rMVP.OutputLog2File = FALSE)

MVP.Data(fileBed=bfilePath, out=tempfile("outfile"), ncpus=1)

options(opts)

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