GEI.prelim: The preliminary data management for GEI (tests for...

In LGEWIS: Tests for Genetic Association/Gene-Environment Interaction in Longitudinal Studies

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

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

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$Y
X<-LGEWIS.example$X
E<-LGEWIS.example$E
time<-LGEWIS.example$time
G<-LGEWIS.example$G

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

LGEWIS documentation built on May 2, 2019, 3:48 p.m.