GGInterScoreTest: Vector of test statistics for gene-gene interaction effects

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

Description

GGInterScoreTest is used to compute the vector of score test statistics for testing the presence of an interaction effect between two genes on a binary phenotype using a continuous or categorical modelling of SNPs.

Usage

GGInterScoreTest(X1, X2, Y, inter.mod = "continuous", perm.method = "parametric", 
                 N = 1000, PC.thresh = 0.05)

Arguments

X1	a n x p1 matrix of genotypes (coded as 0/1/2)
X2	a n x p2 matrix of genotypes (coded as 0/1/2)
Y	a vector of length n containing the values of the binary phenotype (0/1)
inter.mod	a character giving the chosen model for the gene-gene interaction: continuous (inter.mod="continuous") or using dummy coding (inter.mod="dummy")
perm.method	a character giving the chosen resampling method for the phenotype: paramatric bootstrap (perm.method="parametric") or simple permutations (any other character)
N	the number of permutations of the phenotype (default = 1000)
PC.thresh	a threshold for the selection of principal components; only those having an eigenvalue above PC.thresh are selected (default = 0.05)

Value

A list containing the following elements:

Z	the vector of test statistics
Z0	the matrix of permuted vectors of test statistics, displayed as rows
Sigma	the correlation matrix corresponding to Z
Y0	the matrix of permuted phenotypes, displayed as columns
inter.mod	the chosen interaction model ("continuous" or "dummy")
X1	the design matrix corresponding to the first gene
X2	the design matrix corresponding to the second gene
S	the design matrix for the interaction effects
W	the design matrix for the main effects, containing an intercept and the principal components for the main effects
undefined.inter	the indices of the undefined interaction effects, (columns removed from S)
ev	the approximate eigendecomposition of Sigma

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