EmpiricalCalibration (version 3.1.4)

calibrateLlr: Calibrate the log likelihood ratio

Description

calibrateLlr computes calibrated log likelihood ratio using the fitted null distribution

Usage

calibrateLlr(null, likelihoodApproximation, twoSided = FALSE, upper = TRUE)

Value

The calibrated log likelihood ratio.

Arguments

null

An object of class null created using the fitNull function or an object of class mcmcNull created using the fitMcmcNull function.

likelihoodApproximation

Either a data frame containing normal, skew-normal, or custom parametric likelihood approximations, or a list of (adaptive) grid likelihood profiles.

twoSided

Compute two-sided (TRUE) or one-sided (FALSE) p-value?

upper

If one-sided: compute p-value for upper (TRUE) or lower (FALSE) bound?

Examples

data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
null <- fitNull(negatives$logRr, negatives$seLogRr)
positive <- sccs[sccs$groundTruth == 1, ]
calibrateLlr(null, positive)