getFuncRvPosteriors: Posterior probabilities of FR given G and E.

In RIVER: R package for RIVER (RNA-Informed Variant Effect on Regulation)

Description

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).

Usage

getFuncRvPosteriors(Out, probFuncRvFeat, theta)

Arguments

Out	Binary values of outlier status (E).
probFuncRvFeat	probabilities of FR given genomic features and estimated beta, P(FR | G, beta), from getFuncRvFeat.
theta	Current estimate of theta.

Value

posterior probabilities of FR (P(FR | G, E, beta, theta)) and probable status of FR.

Author(s)

Yungil Kim, [e-mail]

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$Outlier))-1) # outlier status (E)
theta.init<-matrix(c(.99, .01, .3, .7), nrow=2)
costs<-c(100, 10, 1, .1, .01, 1e-3, 1e-4)
logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial",
        alpha=0, nfolds=10)
probFuncRvFeat <- getFuncRvFeat(Feat, logisticAllCV$glmnet.fit,
        logisticAllCV$lambda.min)
posteriors <- getFuncRvPosteriors(Out, probFuncRvFeat, theta=theta.init)

RIVER documentation built on Nov. 8, 2020, 6:54 p.m.