outerEpi: Epistasis Detection Outer Chromosomes

In FRGEpistasis: Epistasis Analysis for Quantitative Traits by Functional Regression Model

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.

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

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)

FRGEpistasis documentation built on Nov. 8, 2020, 5:51 p.m.