Epistasis Detection Outer Chromosomes

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Description

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

Usage

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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.

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.

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.

Author(s)

Futao Zhang

Examples

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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)