Epistasis Test by Functional Regression Model

Description

This function is used to analyse the epistasis of genomic region A and genomic region B.

Usage

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frgEpistasisTest(pheno, geno_A, pos_A, geno_B, pos_B)

Arguments

pheno

A vector of phenotype which can be quantitative trait or binary trait.

geno_A

Genotype matrix of gene ( or genomic region) A.

pos_A

Vector of physical positions of SNPs in gene ( or genomic region) A.

geno_B

Genotype matrix of gene ( or genomic region) B.

pos_B

Vector of physical positions of SNPs in gene ( or genomic region) B.

Details

This function is independent with other functions in this package. It is designed for small dataset test. It takes phenotype, genotype and Physical positions as the input. If the position information is NULL, this function considers the SNPs in this gene to be uniformly filled in the gene scope. First this function expanses the genotypes of gene A and gene B. Then it analyses their epistasis.

Value

It returns the p value of chi-square test for epistasis detection between gene A and gene B.

Author(s)

Futao Zhang

Examples

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smp_num=1000
number_snp_A=25
number_snp_B=20
pheno<-sample(c(0:500),smp_num,replace=TRUE)
smpl=rep(0,number_snp_A*smp_num)
idx_1=sample(c(1:(number_snp_A*smp_num)),ceiling(number_snp_A*smp_num/100))
idx_2=sample(c(1:(number_snp_A*smp_num)),ceiling(number_snp_A*smp_num/200))
smpl[idx_1]=1
smpl[idx_2]=2
geno_A=matrix(smpl,smp_num,number_snp_A)

smpl=sample(c(0,1,2),number_snp_B*smp_num,replace=TRUE)
geno_B=matrix(smpl,smp_num,number_snp_B)

frgEpistasisTest(pheno,geno_A,pos_A=NULL,geno_B,pos_B=NULL)