getFuncRvPosteriors {RIVER} | R Documentation |
getFuncRvPosteriors
computes posterior probabilities of functionality
of regulatory variant (FR) given genomic features (G) and outlier
status (E) with current estimate of beta (parameters between FR and G)
and theta (parameters between FR and E).
getFuncRvPosteriors(Out, probFuncRvFeat, theta)
Out |
Binary values of outlier status (E). |
probFuncRvFeat |
probabilities of FR given genomic features and estimated
beta, P(FR | G, beta), from |
theta |
Current estimate of theta. |
posterior probabilities of FR (P(FR | G, E, beta, theta)) and probable status of FR.
Yungil Kim, ipw012@gmail.com
dataInput <- getData(filename=system.file("extdata", "simulation_RIVER.gz", package = "RIVER"), ZscoreThrd=1.5) Feat <- scale(t(Biobase::exprs(dataInput))) # genomic features (G) Out <- as.vector(as.numeric(unlist(dataInput$Outlier))-1) # outlier status (E) theta.init<-matrix(c(.99, .01, .3, .7), nrow=2) costs<-c(100, 10, 1, .1, .01, 1e-3, 1e-4) logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial", alpha=0, nfolds=10) probFuncRvFeat <- getFuncRvFeat(Feat, logisticAllCV$glmnet.fit, logisticAllCV$lambda.min) posteriors <- getFuncRvPosteriors(Out, probFuncRvFeat, theta=theta.init)