R/GetCombinationsOfCorrectandIncorrectPredictions.r

In CausalR: Causal network analysis methods

#' @title returns table of correct and incorrect predictions
#' @description
#' Returns the  numbers of correct and incorrect positive and negative predictions
#' 
#' @param predictionDataStats prediction data statistics table
#' @param experimentalDataStats Experimental data statistics table
#' @return a matrix the  numbers of correct and incorrect positive and negative prediction 
#' 


GetCombinationsOfCorrectandIncorrectPredictions <- function(predictionDataStats, experimentalDataStats) {
    
    numPositivePredictions <- predictionDataStats[1]
    numNegativePredictions <- predictionDataStats[2]
    numUpregulatedGenes <- experimentalDataStats[1]
    numDownregulatedGenes <- experimentalDataStats[2]
    
    # First find bounds for numCorrectPositivePredictions, numIncorrectPositivePredictions, numCorrectNegativePredictions and
    # numIncorrectNegativePredictions
    boundForNumCorrectPositivePredictions <- min(numPositivePredictions, numUpregulatedGenes)
    boundForNumIncorrectPositivePredictions <- min(numPositivePredictions, numDownregulatedGenes)
    boundForNumIncorrectNegativePredictions <- min(numNegativePredictions, numUpregulatedGenes)
    boundForNumCorrectNegativePredictions <- min(numNegativePredictions, numDownregulatedGenes)
    
    # NOTE: Incorrect predictions are those that are predicted positive, but in the results turn out to be negative or vice versa
    
    maxNumberOfRows <- (boundForNumCorrectPositivePredictions + 1) * (boundForNumIncorrectPositivePredictions + 1) * (boundForNumIncorrectNegativePredictions + 
        1) * (boundForNumCorrectNegativePredictions + 1)
    matrixOfPossibleValues <- matrix(0, maxNumberOfRows, 4)
    
    # Let n_pp = possible value for numCorrectPositivePredictions n_pm = possible value for numIncorrectPositivePredictions n_mp = possible value for
    # numIncorrectNegativePredictions n_mm = possible value for numCorrectNegativePredictions (p is used to replace the + and m to replace the -)
    
    # Iterate over possible values of n++, n+-, n-+ and n-- and check if they are valid
    counter = 1
    for (n_pp in 0:boundForNumCorrectPositivePredictions) {
        for (n_pm in 0:boundForNumIncorrectPositivePredictions) {
            for (n_mp in 0:boundForNumIncorrectNegativePredictions) {
                for (n_mm in 0:boundForNumCorrectNegativePredictions) {
                    possibleValues <- c(n_pp, n_pm, n_mp, n_mm)
                    if (CheckPossibleValuesAreValid(predictionDataStats, experimentalDataStats, possibleValues)) {
                        matrixOfPossibleValues[counter, ] <- possibleValues
                        counter = counter + 1
                    }
                }
            }
        }
    }
    matrixOfPossibleValues <- matrixOfPossibleValues[1:counter - 1, ]
    return(matrixOfPossibleValues)
}