tests/testthat/test_GenoGAMSettings-class.R

In gstricker/GenoGAM: A GAM based framework for analysis of ChIP-Seq data

context("Test the GenoGAMSettings-class constructor")

## Unittests
test_that("The GenoGAMSettings constructor works correctly", {
    ggs <- new("GenoGAMSettings")
    test_ggs <- GenoGAMSettings()
    test_ggs@hdf5Control <- list(dir = NULL, level = NULL)
    expect_identical(ggs, test_ggs)
    expect_is(ggs, "GenoGAMSettings")
})

test_that("The GenoGAMSettings validation works correctly", {
    expect_error(GenoGAMSettings(bamParams = "myParams"))
    expect_error(GenoGAMSettings(optimMethod = 10))
    expect_error(GenoGAMSettings(optimControl = 10))
    expect_error(GenoGAMSettings(center = 10))
    expect_error(GenoGAMSettings(chromosomeList = 10))
    expect_error(GenoGAMSettings(processFunction = 10))
    expect_error(GenoGAMSettings(estimControlFunction = 10))
})

test_that("The GenoGAMSettings assignment works correctly", {
    params <- Rsamtools::ScanBamParam(what = c("pos"))
    ggs <- GenoGAMSettings(bamParams = params)
    expect_identical(params, slot(ggs, "bamParams"))
    
    params <- "myOptimMethod"
    ggs <- GenoGAMSettings(optimMethod = params)
    expect_identical(params, slot(ggs, "optimMethod"))

    params <- list(a = 1, b = "2")
    ggs <- GenoGAMSettings(optimControl = params)
    expect_true(all(!(params %in% names(slot(ggs, "optimControl")))))
    
    params <- TRUE
    ggs <- GenoGAMSettings(center = params)
    expect_identical(params, slot(ggs, "center"))

    params <- c("chr1", "chr2")
    ggs <- GenoGAMSettings(chromosomeList = params)
    expect_identical(params, slot(ggs, "chromosomeList"))

    params <- identity
    ggs <- GenoGAMSettings(processFunction = params)
    expect_identical(params, slot(ggs, "processFunction"))

    params <- list(a = 1, b = "2")
    ggs <- GenoGAMSettings(estimControl = params)
    expect_true(all(!(params %in% names(slot(ggs, "estimControl")))))
})