# pointwiseInteraction: Pointwise Interaction Test In FRGEpistasis: Epistasis Analysis for Quantitative Traits by Functional Regression Model

## Description

Test the epistasis of the gene pair by pointwise method

## Usage

 `1` ```pointwiseInteraction(phenoData, x_A, x_B) ```

## Arguments

 `phenoData` Vector of phenotype data which can be quantitative trait or binary trait. `x_A` Matrix of genotype of gene A. `x_B` Matrix of genotype of gene B.

## Details

This function takes phenotype vector and genotype matrices as input and tests the epistasis using pointwise method. For a pair of genes, we assume that the total number of all possible SNP pairs is K (one SNP from one gene and the other SNP from the other gene). The interaction of each SNP pair between the two genes is tested. The minum p value for SNP-SNP interaction among the K pairs is output as the pointwise method result of the gene pair.

## Value

Return the minum p value for SNP-SNP interaction among the K pairs

Futao Zhang

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14``` ```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) pointwiseInteraction(pheno,geno_A,geno_B) ```

FRGEpistasis documentation built on May 2, 2018, 4:45 a.m.