ISIS: To perform GWAS with ISIS EM-BLASSO method

In mrMLM: Multi-Locus Random-SNP-Effect Mixed Linear Model Tools for GWAS

To perform GWAS with ISIS EM-BLASSO method

Description

Iterative Sure Independence Screening EM-Bayesian LASSO

Usage

ISIS(gen,phe,outATCG,genRaw,kk,psmatrix,svpal,svmlod,Genformat,CLO)

Arguments

gen	genotype matrix.
phe	phenotype matrix.
outATCG	genotype for code 1.
genRaw	raw genotype.
kk	kinship matrix.
psmatrix	population structure matrix.
svpal	Critical P-value for selecting variable.
svmlod	Critical LOD score for significant QTN.
Genformat	Format for genotypic codes.
CLO	number of CPU.

Author(s)

Zhang Ya-Wen, Li Pei, Zhang Yuan-Ming
Maintainer: Yuan-Ming Zhang<[e-mail]>

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="ISIS EM-BLASSO",
trait=1)
result=ISIS(InputData$doMR$gen,InputData$doMR$phe,InputData$doMR$outATCG,
InputData$doMR$genRaw,InputData$doMR$kk,InputData$doMR$psmatrix,
0.01,svmlod=3,Genformat=1,CLO=1) 

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