MVP.Data: To prepare data for MVP package

Description

To prepare data for MVP package

Usage

MVP.Data(fileHMP=NULL, fileBed=NULL, fileNum=NULL, filePhe=NULL, fileMap=NULL, fileKin=TRUE,
	filePC=TRUE, out=NULL, sep.hmp="\t", sep.num="\t", sep.map="\t", sep.phe="\t", sep.kin="\t",
	sep.pc="\t", type.geno="char", type.kin="double", type.pc="double", type.map="integer",
	SNP.effect="Add",SNP.impute="Middle", maxLine=10000, maxRecord=1e9, maxInd=1e9, priority="speed", perc=1, pcs.keep=5)

Arguments

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

filePhe

Phenotype, two columns, the first column is taxa name, the second column is trait

fileMap

SNP map information, three columns

fileKin

Kinship, n * n matrix, n is sample size

filePC

the PCA file

out

A marker on output file name

sep.hmp

seperator for files

sep.num

seperator for files

sep.map

seperator for files

sep.phe

seperator for files

sep.kin

seperator for files

sep.pc

seperator for files

type.geno

type parameter in bigmemory, genotype data

type.kin

type parameter in bigmemory, Kinship

type.pc

type parameter in bigmemory, PC

type.map

type parameter in bigmemory, map

SNP.effect

"Add" or "Dom"

SNP.impute

"Left", "Middle", "Right"

maxLine

number of SNPs, only used for saving memory when calculate kinship matrix

maxRecord

maximum number for markers

maxInd

maximum number for individuals

priority

"speed" or "memory"

perc

percentage of total SNPs selected for PCA

pcs.keep

maximum number of PCs