R/HypergeometricTest.R

In mulea: Enrichment Analysis using Multiple Ontologies and False Discovery Rate

#' PRIVATE class : An S4 class to represent a Hypergeometric tests in 
#'   mulea.
#'
#' @slot gmt A data.frame representing the GMT model.
#' @slot element_names Data to be analysed across the model.
#' @slot background_element_names Background data used for the test.
#' @return MuleaHypergeometricTest object. Used as private function.
MuleaHypergeometricTest <- setClass(
    "MuleaHypergeometricTest",
    slots = list(
        gmt = "data.frame",
        element_names = "character",
        pool = "character",
        nthreads = "numeric",
        random_seed = "numeric",
        test = "function"
    )
)

setMethod("initialize", "MuleaHypergeometricTest",
    function(.Object,
        gmt = data.frame(),
        element_names = character(),
        pool = character(),
        nthreads = 4,
        random_seed = 0,
        test = NULL,
        ...) {
            .Object@gmt <- gmt
            .Object@element_names <- element_names
            .Object@pool <- pool
            .Object@nthreads <- nthreads
            .Object@random_seed <- random_seed
            .Object@test <- function(model) {
                model@element_names <- checkIfPoolIncludeSample(model@gmt, 
                    model@element_names, model@pool)

                muleaSetBaseEnrichmentTest <-
                    SetBasedEnrichmentTest(
                        gmt = model@gmt,
                        element_names = model@element_names,
                        pool = model@pool,
                        only_hyper_geometric_test = TRUE,
                        nthreads = model@nthreads,
                        random_seed = model@random_seed
                        )
                muleaSetBaseEnrichmentTestResult <- run_test(
                    muleaSetBaseEnrichmentTest)
                modelGlobal <- model
                testResults <- data.frame(
                    'ontology_name' = 
                        muleaSetBaseEnrichmentTestResult$DB_names,
                    'list_of_values' = model@gmt$list_of_values,
                    'p.value' = muleaSetBaseEnrichmentTestResult$P_val,
                    row.names = NULL
                    )
                testResults
            }
            .Object
        })

#' @describeIn MuleaHypergeometricTest runs test calculations.
#' @param model Object of s4 class represents mulea Test.
#' @return run_test method for MuleaHypergeometricTest object. Used as private
#' function.
setMethod("run_test",
    signature(model = "MuleaHypergeometricTest"),
    function(model) {
        model@test(model)
        })