additive.test(data, response.var, snp.var, exposure.var, main.vars=NULL,
strata.var=NULL, op=NULL)genetic.model, optim.method, indep, maxiter and
reltol (see details). The default is NULL.pval.addP-value of the additive interaction likelihood ratio test.tbThe frequency table defined bytable(snp.var, exposure.var).lm.fullThe output for the full model using a logistic regression model under the
retrospective (indep=TRUE) or the prospective likelihood (indep=FALSE).lm.full.covCovariance matrix for the full model.lm.full.UMLThe glm() output for the full model withsnp.varin the model.lm.baseThe glm() output for the base model withoutsnp.varin the model.optim.outThe optimization output of theoptimfunction for a null model under an additive model restriction.DFThe degrees of freedom of the additive or multiplicative interaction test.LRT.addLikelihood ratio test value for the additive interaction.LRT.multLikelihood ratio test value for the multiplicative interaction.pval.multP-value of the multiplicative interaction likelihood ratio test.pval.wald.multP-value of the multiplicative interaction test (Wald test).pval.UMLP-value of the multiplicative interaction test under the prospective likelihood (Wald test).pval.CMLP-value of the multiplicative interaction test under the retrospective likelihood.
Only applicable forindep=TRUE.pval.EBP-value of the multiplicative interaction test using Empirical Bayes-type shrinkage estimator.
Only applicable forindep=TRUE.method2x2, 2x3, 3x2 or 3x3.or.tbOdds ratio table for the full model without the additive model restriction.SThe output of Synergy Index method for additive interaction under a prospective likelihood
(only applicable for the 2x2 method).APThe output of "Attributable Proportion due to interaction" method for additive interaction under a prospective
likelihood (only applicable for the 2x2 method).RERIThe output of "Relative Excess Risk Due to Interaction" method for additive interaction (only applicable for the 2x2 method).model.infoList of information from the model.Definition of the likelihood under the gene-environment independence assumption: Let D = 0, 1 be the case-control status, G = 0, 1, 2 denote the SNP genotype, S = 1, ..., k denote the levels of the stratification variable and Z be the design matrix for all the covariates including G, the interactions, and a column for the intercept parameter. If $f_s$ denotes the allele frequency for stratum s, then $$P(G = 0) = (1 - f_s)^2$$ $$P(G = 1) = 2f_s(1 - f_s)$$ $$P(G = 2) = f_s^2.$$ If $\xi_s = \log(f_s/(1 - f_s))$, then $$\log \left( \frac{P(G = 1)}{P(G = 0)} \right) = \log(2) + \xi_s$$ and $$\log \left( \frac{P(G = 2)}{P(G = 0)} \right) = 2\xi_s$$
Let $\theta(d,g)=d*Z*\beta+I(g=1)*\log(2)+g*\xi_s.$
Then the likelihood for a subject is $P(D=d, G=g | Z, S) = \frac{\exp(\theta(d, g))}{\sum_{d,g} \exp(\theta(d, g))}$ where the sum is taken over the 6 combinations of d and g.
Options list:
Below are the names for the options list op. All names have default values
if they are not specified.
genetic.model1-3 where 1=dominant, 2=recessive, 3=general.
The default is 3.optim.methodOne of "BFGS", "CG", "L-BFGS-B", "Nelder-Mead", "SANN".
The default is "BFGS".indepTRUE for using a retrospective likelihood for gene-environment independence assumption.
FALSE for using a standard prospective likelihood. The default is FALSE.reltolStopping tolerance. The default is 1e-7.maxiterMaximum number of iterations. The default is 500.Chatterjee, N. and Carroll, R. Semiparametric maximum likelihood estimation exploting gene-environment independence in case-control studies. Biometrika, 2005, 92, 2, pp.399-418.
snp.logistic, snp.score# Use the ovarian cancer data
data(Xdata, package="CGEN")
table(Xdata[, "gynSurgery.history"])
# Recode the exposure variable so that it is 0-1
temp <- Xdata[, "gynSurgery.history"] == 2
Xdata[temp, "gynSurgery.history"] <- 1
# Standard likelihood (indep = FALSE by default)
out1 <- additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history",
main.vars=c("n.children","oral.years"), op=list(genetic.model=1))
# Retrospective likelihood (indep = TRUE) for G by E independence assumption
out2 <- additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history",
main.vars=~n.children+oral.years, strata.var="ethnic.group",
op=list(indep=TRUE, genetic.model=1))Run the code above in your browser using DataLab