getFuncRvFeat: Posterior probabilities of FR given G

Description Usage Arguments Value Author(s) See Also Examples

View source: R/funcRIVER.R

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

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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, [email protected]

See Also

predict

Examples

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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)

ipw012/RIVERpkg documentation built on Feb. 5, 2018, 11:37 p.m.