FRGEpistasis (version 1.8.0)

outerSnpListInteraction: Pairwise Interaction Test Outer The SNP Lists

Description

Test the SNP-SNP interaction. And the SNPs are organized into two different SNP Lists.

Usage

outerSnpListInteraction(pheno, snpList1, snpList2)

Arguments

pheno

Vector of phenotype data.

snpList1

Matrix of the genotypes of all the SNPs on the first SNP list for testing the pairwise interactions.

snpList2

Matrix of the genotypes of all the SNPs on the second SNP list for testing the pairwise interactions.

Value

Return a frame contains names of all the SNPs pairs and p values for interactions of these pairs.

Details

This function aims to test the pairwise interactions between the SNPs organized into different data structures. It takes phenotype and genotypes of the SNPs as the input. And output all the p values for the interactions of SNP pairs.

Examples

snp_list_1 <- as.data.frame(matrix(round(runif(3000,0,2)),1000,3))
snp_list_2 <- as.data.frame(matrix(round(runif(5000,0,2)),1000,5))
colnames(snp_list_1 )<-c("rs10","rs11","rs12")
colnames(snp_list_2 )<-c("rs20","rs21","rs22","rs23","rs24")
pheno<- round(runif(1000,40,60))
outerSnpListInteraction(pheno,snp_list_1,snp_list_2)