MVP.Data {rMVP} | R Documentation

## 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, priority = "speed", 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` | number of SNPs, only used for saving memory when calculate kinship matrix
`priority` | "speed" or "memory"
`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 <- system.file("extdata", "02_bfile", "mvp", package = "rMVP")
    opts <- options(rMVP.OutputLog2File = FALSE)

    MVP.Data(fileBed=bfilePath, out=file.path(tempdir(), "rMVP.test"), ncpus=1)

    options(opts)

[Package rMVP version 0.99.15 Index]