outerEpi {FRGEpistasis} | R Documentation |
Detect epistasis between 2 genes (or genomic regions) which are on different chromosomes.
outerEpi(pheno, gstnd, gStndp, geno_expn, gname, gNamep, gchr, gChrp)
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. |
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.
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.
Futao Zhang
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)