data {roben}R Documentation

simulated data for demonstrating the features of roben

Description

Simulated gene expression data for demonstrating the features of roben.

Usage

data("GxE_small")
data("GxE_large")

Format

GxE_small consists of five components: X, Y, E, clin and coeff. coeff contains the true values of parameters used for generating Y.

GxE_large contains larger datasets: X2, Y2, E2 and clin2

Details

The data model for generating Y

Use subscript ii to denote the iith subject. Let (Xi,Yi,Ei,Clini)(X_{i}, Y_{i}, E_{i}, Clin_{i}), (i=1,,ni=1,\ldots,n) be independent and identically distributed random vectors. YiY_{i} is a continuous response variable representing the disease phenotype. XiX_{i} is the pp–dimensional vector of G factors. The environmental factors and clinical covariates are denoted as the kk-dimensional vector EiE_{i} and the qq-dimensional vector CliniClin_{i}, respectively. The ϵ\epsilon follows some heavy-tailed distribution. Considering the following model:

Yi=α0+t=1qαtClinit+m=1kθmEim+j=1pγjXij+j=1pm=1kζjmEimXij+ϵi,Y_{i} = \alpha_{0} + \sum_{t=1}^{q}\alpha_{t}Clin_{it} + \sum_{m=1}^{k}\theta_{m}E_{im} + \sum_{j=1}^{p}\gamma_{j}X_{ij} + \sum_{j=1}^{p}\sum_{m=1}^{k}\zeta_{jm}E_{im}X_{ij} +\epsilon_{i},

where α0\alpha_{0} is the intercept; αt\alpha_{t}'s, θm\theta_{m}'s, γj\gamma_{j}'s and ζjm\zeta_{jm}'s are the regression coefficients for the clinical covariates, environmental factors, genetic factors and G×\timesE interactions, respectively.

Define βj=(γj,ζj1,,ζjk)(βj1,,βjL)\beta_{j}=(\gamma_{j}, \zeta_{j1},\ldots,\zeta_{jk})^\top \equiv (\beta_{j1},\ldots,\beta_{jL})^\top and Uij=(Xij,XijEi1,XijEik)(Uij1,,UijL)U_{ij}=(X_{ij},X_{ij}E_{i1}\ldots,X_{ij}E_{ik})^\top \equiv (U_{ij1},\dots,U_{ijL})^\top, where L=k+1L=k+1. The model can be written as

Yi=α0+t=1qαtClinit+m=1kθmEim+j=1p(Uijβj)+ϵi,Y_{i} = \alpha_{0} + \sum_{t=1}^{q}\alpha_{t}Clin_{it} + \sum_{m=1}^{k}\theta_{m}E_{im} + \sum_{j=1}^{p} \big(U_{ij}^\top\beta_{j}\big) +\epsilon_{i},

where the coefficient vector βj\beta_{j} represents all the main and interaction effects corresponding to the jjth genetic measurement.

The object coeff in GxE_small is a list of four components, corresponding to α0\alpha_{0}, αt\alpha_{t}'s, θm\theta_{m}'s and βj\beta_{j}'s.

See Also

roben

Examples

data(GxE_small)
dim(X)
print(coeff)

data(GxE_large)
dim(X)
print(coeff)


[Package roben version 0.1.1 Index]