The preliminary data management for GEI (tests for gene-environment interaction)

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Description

Before testing a specific region using a generalized score type test, this function does the preliminary data management, such as pareparing spline basis functions for E etc..

Usage

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GEI.prelim(Y,time,E,X=NULL,E.method='ns',E.df=floor(sqrt(length(unique(time[,1])))),
corstr="exchangeable")

Arguments

Y

The outcome variable, an n*1 matrix where n is the total number of observations

time

An n*2 matrix describing how the observations are measured. The first column is the subject id. The second column is the measured exam (1,2,3,etc.).

E

An n*1 environmental exposure.

X

An n*p covariates matrix where p is the total number of covariates.

E.method

The method of sieves for the main effect of E. It can be "ns" for natural cubic spline sieves; "bs" for B-spline sieves; "ps" for polynomial sieves. The default is "ns".

E.df

Model complexity for the method of sieves, i.e., number of basis functions. The default is sqrt(m).

corstr

The working correlation as specified in 'geeglm'. The following are permitted: "independence", "exchangeable", "ar1".

Value

It returns a list used for function GEI.test().

Examples

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library(LGEWIS)

# Load data example
# Y: outcomes, n by 1 matrix where n is the total number of observations
# X: covariates, n by p matrix
# E: environmental exposure, n by 1 matrix
# time: describe longitudinal structure, n by 2 matrix
# G: genotype matrix, m by q matrix where m is the total number of subjects

data(LGEWIS.example)
Y<-LGEWIS.example$Y;time<-LGEWIS.example$time;
E<-LGEWIS.example$E;X<-LGEWIS.example$X;G<-LGEWIS.example$G

# Preliminary data management
result.prelim<-GEI.prelim(Y,time,E,X=X)