Epistasis Detection Inner one Chromosome

Share:

Description

Detect epistasis between 2 genes (or genomic regions) both of which are on the same chromosome.

Usage

1
innerEpi(pheno, gstnd, geno_expn, gname, gchr)

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 current chromosome in the matrix "geno_expn".

geno_expn

Matrix of expansed genotype data of all the genes.

gname

Vector of gene names on current chromosome.

gchr

Vector of Chromosome number of current chromosome.

Details

This function tests the epistasis between 2 genes both of which are on the same chromosome. 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

1
2
3
4
5
6
7
8
9
smp_num<-1000
number_basis<-9
pheno<-sample(c(0:500),smp_num,replace=TRUE)
gname<-c("g1","g2")
gstnd<-c(0,5,9)
smpl<-runif(number_basis*smp_num, 0.0, 1.0)
geno_expn<-matrix(smpl,smp_num,number_basis)
gchr<-c(1,1)
innerEpi(pheno,gstnd,geno_expn,gname,gchr)