convertNullToErrorModel {EmpiricalCalibration}

Convert empirical null distribution to systematic error model

Description

This function converts an empirical null distribution, fitted using estimates only for negative controls, into a systematic error distribution that can be used to calibrate confidence intervals in addition to p-values.

Whereas the fitSystematicErrorModel uses positive controls to determine how the error distribution changes with true effect size, this function requires the user to make an assumption. The default assumption, meanSlope = 1 and sdSlope = 0, specify a belief that the error distribution is the same for all true effect sizes. In many cases this assumption is likely to be correct, however, if an estimation method is biased towards the null this assumption will be violated, causing the calibrated confidence intervals to have lower than nominal coverage.

Usage

convertNullToErrorModel(null, meanSlope = 1, sdSlope = 0)

Arguments

null

The empirical null distribution fitted using either the fitNull or the fitMcmcNull function.

meanSlope

The slope for the mean of the error distribution. A slope of 1 means the error is the same for different values of the true relative risk.

sdSlope

The slope for the log of the standard deviation of the error distribution. A slope of 0 means the standard deviation is the same for different values of the true relative risk.

Value

An object of type systematicErrorModel.

Examples

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