GE_test_moment_calcs: GE_test_moment_calcs.R

Description Usage Arguments Value Examples

View source: R/GE_test_moment_calcs.R

Description

Test function mostly for internal use to ensure the higher order moments (covariances) calculated in GE_bias_normal_squaredmis() are correct. Will give warning messages if some calculations appear to be incorrect. If receive warning messages, run again, and if still receive the same warning messages, something may be wrong.

Usage

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GE_test_moment_calcs(beta_list, rho_list, prob_G, cov_Z = NULL,
  cov_W = NULL, num_sub = 2e+06, test_threshold = 0.003, 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.

rho_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).

prob_G

Probability that each allele is equal to 1. Since each SNP has two alleles, the expectation of G is 2*prob_G. Should be a d*1 vector.

cov_Z

Should be a matrix equal to cov(Z) or NULL. Must be specified if Z is a vector.

cov_W

Should be a matrix equal to cov(W) or NULL. Must be specified if W is a vector.

num_sub

Number of subjects to simulate/test with.

test_threshold

How close does our simulated value have to be to the analytic value?

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.

Value

Nothing

Examples

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GE_test_moment_calcs(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 Aug. 10, 2017, 1:03 a.m.