R/GetRowAndColumnSumValues.r

In CausalR: Causal network analysis methods

#' @title  get row and column sum values
#' @description
#' Returns the possible values of r+, r-, c+ and c- (the column and row sum values) following page 6 of Assessing
#' statistical  significance in causal graphs (Chindelevitch et. al)
#' @param predictionListStats a vector containing the number of postive, negative, or non-signficant/contradictory predictions (q+, q- and q0)
#' @param experimentalResultStats a vector containing the number of postive, negative, or non-signficant/contradictory observations (n+, n- and n0)
#' @return a matrix of row and sum values r+, r-, c+ and c- 


#' @references
#' L Chindelevitch et al.
#' Assessing statistical significance in causal graphs.
#' BMC Bioinformatics, 13(35), 2012.



GetRowAndColumnSumValues <- function(predictionListStats, experimentalResultStats) {
    
    
    # Number of positive predictions from the network. This will be an upper bound for r+ (r_p)
    q_p <- predictionListStats[1]
    # Number of negative predictions from the network. This will be an upper bound for r- (r_m)
    q_m <- predictionListStats[2]
    # Number of positive results. This will be an upper bound for c+ (c_p)
    n_p <- experimentalResultStats[1]
    # Number of negative results. This will be an upper bound for c- (c_m)
    n_m <- experimentalResultStats[2]
    
    # Pre-declare an array to store the valid column/row sum values - since we only iterate over three quantities, the array can have a maximum size
    # equal to the product of the three smallest values out of q_p+1, q_m+1, n_p+1, and n_m+1.
    maximumValue = max(q_p + 1, q_m + 1, n_p + 1, n_m + 1)
    maxNumberOfRows <- (q_p + 1) * (q_m + 1) * (n_p + 1) * (n_m + 1)/maximumValue
    tryCatch({
        possibleRowAndColumnSumValues <- matrix(0, maxNumberOfRows, 4)
        # Iterate all possible values of r+, r-, c+ and c- and check if they produce a valid contingency table
        counter <- 1
        for (r_p in 0:q_p) {
            # for 0 to the limit of negative predictions
            for (r_m in 0:q_m) {
                # for 0 to the limit of number of positive results
                for (c_p in 0:n_p) {
                    # calculate the column sum of m
                    c_m <- r_p + r_m - c_p
                    rowAndColumnSumValues <- c(r_p, r_m, c_p, c_m)
                    if (CheckRowAndColumnSumValuesAreValid(rowAndColumnSumValues, predictionListStats, experimentalResultStats)) {
                        if (counter > maxNumberOfRows) {
                            # double the size of the matrix if it doesn't have any space
                            possibleRowAndColumnSumValues <- matrix(c(possibleRowAndColumnSumValues, matrix(0, maxNumberOfRows, 4)), ncol = 4)
                        }
                    possibleRowAndColumnSumValues[counter, ] <- rowAndColumnSumValues
                    counter <- counter + 1
                    }
                }
            }
        }
        
        # Only want to keep the rows that were populated in the set of for loops above
        possibleRowAndColumnSumValues <- possibleRowAndColumnSumValues[1:counter - 1, ]
        
        return(possibleRowAndColumnSumValues)
    }, error = function(e) {
        # If there is an error, report back all valuable information to the user - this is deisgned for when there is a memory error.
        print(e)
        print(paste("Number of positive predictions:", predictionListStats[1]))
        print(paste("Number of negative predictions:", predictionListStats[2]))
        print(paste("Number of ambiguous/unknown predictions:", predictionListStats[3]))
        print(paste("Number of upregualted results:", experimentalResultStats[1]))
        print(paste("Number of down-regualted results:", experimentalResultStats[2]))
        print(paste("Number of non-significantly changed results:", experimentalResultStats[3]))
        print(paste("Number of rows in array to store all the combinations of row and column sums in upper 2x2 submatrix of contingency table:", maxNumberOfRows))
        stop()
    })
}