caThreshold <- function(userFormula,
new_covariates,
diseaseData = NULL,
controlData = NULL,
control_sensitivity = NULL,
control_specificity = NULL) {
if (is.null(control_sensitivity) & is.null(control_specificity)) {
stop("Give a sensitivity/specificity to control at!")
} else if (!is.null(control_sensitivity) & !is.null(control_specificity)) {
stop("Sensitivity and specificity cannot be controlled at the same time!")
} else if (!is.null(control_sensitivity)) {
if(is.null(diseaseData)) {
stop("I need data from patients (diseaseData)!")
} else {
cathres <- caThreshold_at_sensitivity(diseaseData = diseaseData,
userFormula = userFormula,
control_sensitivity = control_sensitivity,
new_covariates = new_covariates)
}
} else if (!is.null(control_specificity)) {
if(is.null(controlData)) {
stop("I need data from normal controls (controlData)!")
} else {
cathres <- caThreshold_at_specificity(controlData = controlData,
userFormula = userFormula,
control_specificity = control_specificity,
new_covariates = new_covariates)
}
}
return(cathres)
}
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