FRGEpistasis (version 1.8.0)

outerEpi: Epistasis Detection Outer Chromosomes

Description

Detect epistasis between 2 genes (or genomic regions) which are on different chromosomes.

Usage

outerEpi(pheno, gstnd, gStndp, geno_expn, gname, gNamep, gchr, gChrp)

Arguments

pheno

Vector of phenotype data which can be quantitative trait or binary trait.

gstnd

Vector of indexes which indicates the start indexes and end indexes of expansed genotype of each gene on one chromosome in the matrix "geno_expn".

gStndp

Vector of indexes which indicates the start indexes and end indexes of expansed genotype of each gene on the other chromosome in the matrix "geno_expn".

geno_expn

Matrix of expansed genotype data of all the genes.

gname

Vector of gene names on one chromosome.

gNamep

Vector of gene names on the other chromosome.

gchr

Vector of Chromosome number of one chromosome.

gChrp

Vector of Chromosome number of the other chromosome.

Value

Return a matrix which contains the gene names of the gene pairs and the p values of chi-squared test for the epistasis of the gene pairs.

Details

This function tests the epistasis between 2 genes which are on different chromosomes. It takes expansed genotype data as the input. First the data of the gene are extracted from "geno_expn" with "gstnd" and "gname". Then the function "fRGInteraction" will be called.

Examples

smp_num=1000
number_basis<-40
pheno<-sample(c(0:500),smp_num,replace=TRUE)
gname<-c("g1","g2")
gNamep<-c("r1","r2","r3")
gstnd<-c(0,5,9)
gStndp<-c(16,23,29,36)
smpl<-runif(number_basis*smp_num, 0.0, 1.0)
geno_expn<-matrix(smpl,smp_num,number_basis)
gchr<-c(1,1)
gchrp<-c(3,3,3)
outerEpi(pheno,gstnd,gStndp,geno_expn,gname,gNamep,gchr,gchrp)