R/CalculateSignificance.r

In CausalR: Causal network analysis methods

#' @title calculate overall significance p-value
#' @description
#' Calculates the p-value of a score given the hypothesis score and the 
#' distribution table, using either the quartic or the (faster) cubic algorithm

#' @export
#' @concept CausalR
#' @param hypothesisScore score for a particular hypothesis 
#' @param predictionListStats numbers of predicted up-regulated, 
#' predicted down-regulated and ambiguous predictions predicted by the algorithm 
#' @param experimentalResultStats numbers of up-regulated, 
#' down-regulated and not significantly changed transcripts in the 
#' experimental data 
#' @param epsilon threshold that is used when calculating the p-value 
#' using the cubic algorithm 
#' @param useCubicAlgorithm  use the cubic algorithm, defaults to TRUE
#' @param use1bAlgorithm  use the 1b version of the algorithm, defaults to TRUE
#' used to calculate the p-value
#' @return the resulting  p-value
#' @examples
#' CalculateSignificance(5, c(7,4,19), c(6,6,18))
#' CalculateSignificance(5, c(7,4,19), c(6,6,18), useCubicAlgorithm=TRUE)
#' CalculateSignificanceUsingQuarticAlgorithm(5, c(7,4,19), c(6,6,18))
#' CalculateSignificance(5, c(7,4,19), c(6,6,18), useCubicAlgorithm=FALSE)
#' CalculateSignificance(5, c(7,4,19), c(6,6,18), 1e-5)
#' CalculateSignificance(5, c(7,4,19), c(6,6,18), epsilon=1e-5, useCubicAlgorithm=TRUE)
#' CalculateSignificanceUsingCubicAlgorithm(5, c(7,4,19), c(6,6,18), 1e-5)



CalculateSignificance <- function(hypothesisScore, predictionListStats, experimentalResultStats, epsilon = 1e-05, useCubicAlgorithm = TRUE, use1bAlgorithm = TRUE) {
    
    if (useCubicAlgorithm) {
        if (use1bAlgorithm) {
            pValue <- CalculateSignificanceUsingCubicAlgorithm1b(hypothesisScore, predictionListStats, experimentalResultStats, epsilon)
        } else {
            pValue <- CalculateSignificanceUsingCubicAlgorithm(hypothesisScore, predictionListStats, experimentalResultStats, epsilon)
        }
    } else {
        pValue <- CalculateSignificanceUsingQuarticAlgorithm(hypothesisScore, predictionListStats, experimentalResultStats)
    }
    return(pValue)
}