GE_translate_inputs: GE_translate_inputs.R

In GEint: Misspecified Models for Gene-Environment Interaction

GE_translate_inputs.R

Description

Mostly for internal use, function called by GE_bias_normal() and GE_scoreeq_sim() to translate the rho_list inputs and return a total covariance matrix for simulation/ checking validity of covariance structure. If invalid covariance structure, will stop and return an error message.

Usage

GE_translate_inputs(beta_list, rho_list, prob_G, cov_Z = NULL,
  cov_W = NULL, corr_G = NULL)

Arguments

beta_list	A list of the effect sizes in the true model. Use the order beta_0, beta_G, beta_E, beta_I, beta_Z, beta_M. If G or Z or M is a vector, then beta_G/beta_Z/beta_M should be vectors. If Z and/or M/W do not exist in your model, then set beta_Z and/or beta_M = 0.
prob_G	Probability that each allele is equal to 1. Since each SNP has two alleles, the expectation of G is 2*prob_G.
cov_Z	Should be a matrix equal to cov(Z) or NULL if no Z.
cov_W	Should be a matrix equal to cov(W) or NULL if no W.
corr_G	Should be a matrix giving the *pairwise correlations* between each SNP in the set, or NULL. Must be specified if G is a vector. For example, the [2,3] element of the matrix would be the pairwise correlation between SNP2 and SNP3. Diagonal should be 1.
cov_list	A list of expectations (which happen to be covariances if all covariates are centered at 0) in the order specified by GE_enumerate_inputs(). If Z and/or M/W do not exist in your model, then treat them as constants 0. For example, if Z doesn't exist and W includes 2 covariates, then set cov(EZ) = 0 and cov(ZW) = (0,0). If describing expectations relating two vectors, i.e. Z includes two covariates and W includes three covariates, sort by the first term and then the second. Thus in the example, the first three terms of cov(ZW) are cov(Z_1,W_1),cov(Z_1,W_2), cov(Z_1,W_3), and the last three terms are cov(Z_3,W_1), cov(Z_3,W_2), cov(Z_3,W_3).

Value

A list with the elements:

sig_mat_total

The sigma parameter for rmvnorm call to generate our data.

Examples

GE_translate_inputs( beta_list=as.list(runif(n=6, min=0, max=1)),
rho_list=as.list(rep(0.3,6)), prob_G=0.3, cov_Z=1, cov_W=1)

GEint documentation built on May 18, 2022, 9:05 a.m.