Test posterior probabilities of FR given G and E

Description

testPosteriors computes posterior probabilities of FR (functionality of regulatory variant) given G (genomic annotations) and E (outlier status) with estimate of beta (parameters between FR and G) and theta (parameters between FR and E).

Usage

testPosteriors(Feat, Out, emModel)

Arguments

Value

test posterior probabilities of FR given new outlier status (E) and genomic features (G), P(FR | G, E, beta, theta), and probable status of FR.

Author(s)

Yungil Kim, ipw012@gmail.com

See Also

getFuncRvFeat and getFuncRvPosteriors

Examples

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$Outlier))-1) # outlier status (E)
theta.init <- matrix(c(.99, .01, .3, .7), nrow=2)
costs <- c(100, 10, 1, .1, .01, 1e-3, 1e-4)
logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial",
        alpha = 0, nfolds=10)
emModelAll <- integratedEM(Feat, Out, logisticAllCV$lambda.min, logisticAllCV$glmnet.fit,
        pseudoc=50, theta.init, costs, verbose=FALSE)
trainedpost <- testPosteriors(Feat, Out, emModel=emModelAll)