getFuncRvFeat {RIVER}R Documentation

Posterior probabilities of FR given G

Description

getFuncRvFeat computes posterior probabilities of FR (functionality of regulatory variant) given G (genomic features) and current estimate of beta (parameters between FR and G).

Usage

getFuncRvFeat(Feat, logistic.model, lambda)

Arguments

Feat

Genomic features (G)

logistic.model

Logistic regression model with current estimate of beta

lambda

Selected lambda

Value

probabilities of FR given genomic features, P(FR | G)

Author(s)

Yungil Kim, ipw012@gmail.com

See Also

predict

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$Outlier))-1) # outlier status (E)
costs <- c(100, 10, 1, .1, .01, 1e-3, 1e-4)
logisticAllCV <- glmnet::cv.glmnet(Feat, Out, lambda=costs, family="binomial",
        alpha = 0, nfolds=10)
probFuncRvFeat <- getFuncRvFeat(Feat, logistic.model=logisticAllCV$glmnet.fit,
        lambda=logisticAllCV$lambda.min)


[Package RIVER version 1.16.0 Index]