innerEpi {FRGEpistasis} | R Documentation |
Detect epistasis between 2 genes (or genomic regions) both of which are on the same chromosome.
innerEpi(pheno, gstnd, geno_expn, gname, gchr)
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. |
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.
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<-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)