pLARmEB: To perform GWAS with pLARmEB method
In mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

pLARmEB

R Documentation

To perform GWAS with pLARmEB method

Description

polygene-background-control-based least angle regression plus Empirical Bayes

Usage

pLARmEB(gen,phe,outATCG,genRaw,kk,psmatrix,CriLOD,lars1,Genformat,Bootstrap,CLO)

Arguments

`gen`	genotype matrix.
`phe`	phenotype matrix.
`outATCG`	genotype for code 1.
`genRaw`	raw genotype.
`kk`	kinship matrix.
`psmatrix`	population structure matrix.
`CriLOD`	Critical LOD score for significant QTN.
`lars1`	No. of potentially associated variables selected by LARS.
`Genformat`	Format for genotypic codes.
`Bootstrap`	Bootstrap=FALSE indicates the analysis of only real dataset, Bootstrap=TRUE indicates the analysis of both real dataset and four resampling datasets.
`CLO`	number of CPU.

Author(s)

Zhang Ya-Wen, Wang Jing-Tian, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<soyzhang@mail.hzau.edu.cn>

Examples

G1=data(Gen)
P1=data(Phe)
Readraw=ReadData(fileGen=Gen,filePhe=Phe,fileKin=NULL,filePS =NULL,
Genformat=1)
InputData=inputData(readraw=Readraw,Genformat=1,method="pLARmEB",trait=1)
result=pLARmEB(InputData$doMR$gen,InputData$doMR$phe,InputData$doMR$outATCG,
InputData$doMR$genRaw,InputData$doMR$kk,InputData$doMR$psmatrix,
CriLOD=3,lars1=20,Genformat=1,Bootstrap=FALSE,CLO=1)

mrMLM documentation built on March 27, 2022, 9:05 a.m.