GeneGeneInteractions-package: Global tests for the detection of gene-gene interaction...

In fhebert/GeneGeneInteractions2: Global tests for the detection of gene-gene interaction effects on binary phenotypes

Description

The GeneGeneInteractions package provides functions to compute global p-values for the detection of gene-gene interaction effects on a binary phenotype. It also provides a function to generate samples of genotype and phenotype values under a gene-gene interaction logistic model.

Author(s)

Florian Hébert, Mathieu Emily, David Causeur

Maintainer: Florian Hébert <[e-mail]>

See Also

GGInterScoreTest SampleGGInter OmniGGInterTest GBDCorTest

Examples

#Matrices of genotypes for 2 genes, for a population of 100,000 individuals
X1 = matrix(rbinom(10*100000,2,0.4),ncol=10)
X2 = matrix(rbinom(10*100000,2,0.4),ncol=10)

#Sample of genotype and phenotype values. No main effects, interaction effect between:
#SNP 3 of gene 1 and SNP 7 of gene 2 
#SNP 4 of gene 1 and SNP 6 of gene 2 
#Dominant-dominant interaction effect
coef = rep(0.2,4)
I = matrix(c(3,7,4,6),ncol=2,byrow=TRUE)
tmp = SampleGGInter(X1,X2,-3,0,1,0,1,matrix(rep(coef,2),ncol=4,byrow=TRUE),I,1000,1000)

#Score test statistics (continuous and dummy-coding based models)
test.cont = GGInterScoreTest(tmp$SNP1,tmp$SNP2,tmp$Phenotype,inter.mod="continuous")
test.dummy = GGInterScoreTest(tmp$SNP1,tmp$SNP2,tmp$Phenotype,inter.mod="dummy")

#Omnibus tests
res = OmniGGInterTest(tmp$SNP1,tmp$SNP2,tmp$Phenotype)

fhebert/GeneGeneInteractions2 documentation built on May 19, 2019, 12:36 a.m.