R/PopulateTwoByTwoContingencyTable.r

In CausalR: Causal network analysis methods

#' @title Populate Two by Two Contingency Table
#' @description
#' Calculates a 2x2 contingency table.
#' Given the value of n++ and the row and column sums (r+, r-, c+, c-),
#' Calculates the remaining values in the 2x2 contingency table i.e.
#' n+-, n-+, and n--. See Chindelevich et al. BMC Bioinformatics (2012) paper 
#' 'Assessing Statistical significance of causal graphs' for clarification on notation.

#' @param rowAndColumnSumValues the row and column sums (r+, r-, c+, c-).
#' @param n_pp the value of n++.
#' @return  the completed 2x2 contingency table: n++, n+-, n-+, n--

#' @references
#' L Chindelevitch et al.
#' Causal reasoning on biological networks: Interpreting transcriptional changes.
#' Bioinformatics, 28(8):1114-21, 2012.   

PopulateTwoByTwoContingencyTable <- function(rowAndColumnSumValues, n_pp) {
    
    # r+
    r_p <- rowAndColumnSumValues[1]
    # r-
    r_m <- rowAndColumnSumValues[2]
    # c+
    c_p <- rowAndColumnSumValues[3]
    # c- c_m <- rowAndColumnSumValues[4]
    
    # n+-
    n_pm <- r_p - n_pp
    # n-+
    n_mp <- c_p - n_pp
    # n--
    n_mm <- r_m - n_mp
    
    contingencyTableValues <- c(n_pp, n_pm, n_mp, n_mm)
    return(contingencyTableValues)
}