mvp (version 1.0.1)

MVP.MLM: To perform GWAS with MLM model and get the P value of SNPs

Description

To perform GWAS with MLM model and get the P value of SNPs

Usage

MVP.MLM(phe, geno, K=NULL, CV=NULL, REML=NULL, priority="speed", genoName=NULL, cpu=2, vc.method="EMMA",
	maxLine=1000, file.output=TRUE, memo="MVP")

Arguments

phe

phenotype, n * 2 matrix

geno

genotype, m * n, m is marker size, n is population size

CV

covariates

K

Kinship, Covariance matrix(n * n) for random effects; must be positive semi-definite

REML

a list that contains ve and vg

priority

speed or memory

genoName

name of genotype file, when priority is memory, it is used for attach bigmatrix under windows platform

cpu

number of cpus used for parallel computation

vc.method

the methods for estimating variance component("emma" or "gemma")

maxLine

when the priority is 'memory', users can change this parameter to limit the memory

file.output

whether to output files or not

memo

a marker on output file name