inst/unitTests/test_methylInheritanceInternalMethods.R

In methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

###################################################
# Created by Astrid Deschenes
# 2017-01-09
###################################################

###################################################
## Test the methylInheritanceInternalMethods functions
###################################################


library("GenomicRanges")

METHYL_OBJ_FILE <- system.file("extdata", "methylObj_001.RDS",
                                package = "methylInheritance")

METHYL_OBJ <- readRDS(METHYL_OBJ_FILE)

data(methylInheritanceResults)

.tearDown <- function() {
    if (dir.exists("test_001")) {
        unlink("test_001", recursive = TRUE, force = TRUE)
    }
}


###########################################################
## runOnePermutationOnAllGenerations() function
###########################################################

## Test sites when all parameters are valid
test.validateRunPermutationUsingMethylKitInfo_sites_good_01 <- function() {
    ## Extract information
    set.seed(111)
    allSamples <- sample(unlist(METHYL_OBJ, recursive = FALSE), 36, replace = F)
    treatment <- c(0,0,0,0,0,0,1,1,1,1,1,1)
    sampleList01 <- new("methylRawList", allSamples[1:12],
                        treatment = treatment)
    sampleList02 <- new("methylRawList", allSamples[13:24],
                        treatment = treatment)
    sampleList03 <- new("methylRawList", allSamples[25:36],
                        treatment = treatment)
    input <- list(sampleList01, sampleList02, sampleList03)

    if (!dir.exists("test_001")) {
        dir.create("test_001/SITES/", recursive = TRUE)
    }

    obs <- methylInheritance:::runOnePermutationOnAllGenerations(
        id = 1, methylInfoForAllGenerations = input, outputDir = "test_001/", type = "sites",
        nbrCoresDiffMeth = 1,
        minReads = 10, minMethDiff = 10, qvalue = 0.05,
        maxPercReads = 99.9, destrand = FALSE, minCovBasesForTiles = 2,
        tileSize = 1000, stepSize = 100, restartCalculation = FALSE, saveInfoByGeneration = FALSE)

    exp <- list()
    exp[["SITES"]] <- list()
    exp[["SITES"]][["i2"]] <- list()
    exp[["SITES"]][["i2"]][["HYPER"]] <- list(0,0)
    exp[["SITES"]][["i2"]][["HYPO"]]  <- list(3,0)
    exp[["SITES"]][["iAll"]][["HYPER"]]  <- list(0)
    exp[["SITES"]][["iAll"]][["HYPO"]]   <- list(0)

    obsV <- methylInheritance::loadAllRDSResults(permutationResultsDir = "test_001", analysisResultsDir = NULL)

    message <- paste0(" test.validateRunPermutationUsingMethylKitInfo_sites_good_01() ",
                    "- Valid parameters did not generated expected results.")

    checkEquals(obs, 0, msg = message)
    checkEquals(obsV$PERMUTATION[[1]], exp, msg = message)
}

## Test tiles when all parameters are valid
# test.validateRunPermutationUsingMethylKitInfo_tiles_good_01 <- function() {
#     ## Extract information
#     set.seed(11)
#     allSamples <- sample(unlist(METHYL_OBJ, recursive = FALSE), 36,
#                             replace = F)
#     treatment <- c(0,0,0,0,0,0,1,1,1,1,1,1)
#     sampleList01 <- new("methylRawList", allSamples[1:12],
#                             treatment = treatment)
#     sampleList02 <- new("methylRawList", allSamples[13:24],
#                             treatment = treatment)
#     sampleList03 <- new("methylRawList", allSamples[25:36],
#                             treatment = treatment)
#     input <- list(sampleList01, sampleList02, sampleList03)
#
#     obs <- tryCatch(methylInheritance:::runOnePermutationOnAllGenerations(
#         id = 2,
#         methylInfoForAllGenerations = input, outputDir = NULL, type = "tiles",
#         nbrCoresDiffMeth = 1,
#         minReads = 5, minMethDiff = 5, qvalue = 0.05,
#         maxPercReads = 99.9, destrand = FALSE, minCovBasesForTiles = 2,
#         tileSize = 1000, stepSize = 100, restartCalculation = FALSE),
#         error=conditionMessage)
#
#     exp <- list()
#     exp[["TILES"]] <- list()
#     exp[["TILES"]][["i2"]] <- list()
#     exp[["TILES"]][["i2"]][["HYPER"]] <- list(0, 0)
#     exp[["TILES"]][["i2"]][["HYPO"]]  <- list(1900, 0)
#     exp[["TILES"]][["iAll"]][["HYPER"]]  <- list(0)
#     exp[["TILES"]][["iAll"]][["HYPO"]]   <- list(0)
#
#     message <- paste0(" test.validateRunPermutationUsingMethylKitInfo_tiles_good_01() ",
#                 "- Valid parameters did not generated expected results.")
#
#     checkEquals(obs, exp, msg = message)
# }

###########################################################
## isInterGenerationResults() function
###########################################################

test.isInterGenerationResults_true <- function() {

    filesDir <- system.file("extdata", "TEST", package="methylInheritance")

    obs <- methylInheritance:::isInterGenerationResults(outputDir =
                paste0(filesDir, "/"), 0, "sites")

    message <- paste0("test.isInterGenerationResults_true() ",
                      "- Function should return TRUE")

    checkTrue(obs, msg = message)
}


###########################################################
## validateExtractInfo() function
###########################################################

test.validateExtractInfo_position_zero <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = methylInheritanceResults, type = "sites",
        inter = "i2", position = 0),
        error=conditionMessage)

    exp <- "position must be a positive integer"

    message <- paste0("test.validateExtractInfo_position_zero() - ",
                      "Zero position value did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_position_string <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = methylInheritanceResults, type = "sites",
        inter = "i2", position = "hi"),
        error=conditionMessage)

    exp <- "position must be a positive integer"

    message <- paste0("test.validateExtractInfo_position_string() - ",
                      "Zero position value did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_allResults_vector <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = c(1,2,3), type = "sites",
        inter = "i2", position = 1),
        error=conditionMessage)

    exp <- "allResults must be of class \"methylInheritanceAllResults\""

    message <- paste0("test.validateExtractInfo_allResults_vector() - ",
                      "allResults vector did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_type_wrong <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = methylInheritanceResults, type = "toto",
        inter = "i2", position = 1),
        error=conditionMessage)

    exp <- "allResults must have an element called \"TOTO\" in its \"OBSERVATION\" list"

    message <- paste0("test.validateExtractInfo_type_wrong() - ",
                      "Wrong type did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_type_wrong <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = methylInheritanceResults, type = "sites",
        inter = "hi", position = 1),
        error=conditionMessage)

    exp <- "allResults must have an element called \"hi\" in the \"SITES\" list present in its \"OBSERVATION\" list"

    message <- paste0("test.validateExtractInfo_type_wrong() - ",
                      "Wrong inter did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_position_too_high <- function() {
    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = methylInheritanceResults, type = "sites",
        inter = "i2", position = 4),
        error=conditionMessage)

    exp <- "position must correspond to a valid entry in the \"allResults$OBSERVATION[[SITES]][[i2]]\""

    message <- paste0("test.validateExtractInfo_position_too_high() - ",
                      "Too high position value did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_allResults_no_permutation <- function() {
    g<-list()
    g[["OBSERVATION"]] <- methylInheritanceResults$OBSERVATION
    class(g)<-"methylInheritanceAllResults"

    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = g, type = "sites",
        inter = "i2", position = 1),
        error=conditionMessage)

    exp <- "allResults must have an element called \"PERMUTATION\""

    message <- paste0("test.validateExtractInfo_allResults_no_permutation() - ",
                      "allResult without permutation value did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_allResults_no_observation <- function() {
    g<-list()
    g[["PERMUTATION"]] <- methylInheritanceResults$OBSERVATION
    class(g)<-"methylInheritanceAllResults"

    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = g, type = "sites",
        inter = "i2", position = 1),
        error=conditionMessage)

    exp <- "allResults must have an element called \"OBSERVATION\""

    message <- paste0("test.validateExtractInfo_allResults_no_observation() - ",
                      "allResult without observation value did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateExtractInfo_allResults_not_list <- function() {
    g<-vector()
    class(g)<-"methylInheritanceAllResults"

    obs <- tryCatch(methylInheritance:::validateExtractInfo(
        allResults = g, type = "sites",
        inter = "i2", position = 1),
        error=conditionMessage)

    exp <- "allResults must be a list"

    message <- paste0("test.validateExtractInfo_allResults_not_list() - ",
                      "allResult not list did not generated expected message.")

    checkEquals(obs, exp, message)
}

###########################################################
## validateLoadConvergenceData() function
###########################################################

test.validateLoadConvergenceData_integer_analysisDir <- function() {
    obs <- tryCatch(methylInheritance:::validateLoadConvergenceData(analysisResultsDir = 33,
            permutationResultsDir = "./", position = 1, by = 2),
            error=conditionMessage)

    exp <- "analysisResultsDir must be a character string"

    message <- paste0("test.validateLoadConvergenceData_integer_analysisDir() - ",
                      "Integer as analysis directory did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateLoadConvergenceData_integer_permutationDir <- function() {
    obs <- tryCatch(methylInheritance:::validateLoadConvergenceData(analysisResultsDir = "./",
                    permutationResultsDir = 44, position = 1, by = 2),
                    error=conditionMessage)

    exp <- "permutationResultsDir must be a character string"

    message <- paste0("test.validateLoadConvergenceData_integer_permutationDir() - ",
                      "Integer as permutation directory did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateLoadConvergenceData_position_zero <- function() {
    obs <- tryCatch(methylInheritance:::validateLoadConvergenceData(analysisResultsDir = "./",
                        permutationResultsDir = "./", position = 0, by = 2),
                    error=conditionMessage)

    exp <- "position must be a positive integer"

    message <- paste0("test.validateLoadConvergenceData_position_zero() - ",
                      "Zero as position did not generated expected message.")

    checkEquals(obs, exp, message)
}

test.validateLoadConvergenceData_by_zero <- function() {
    obs <- tryCatch(methylInheritance:::validateLoadConvergenceData(analysisResultsDir = "./",
                permutationResultsDir = "./", position = 1, by = 0),
                error=conditionMessage)

    exp <- "by must be a positive integer"

    message <- paste0("test.validateLoadConvergenceData_by_zero() - ",
                      "Zero as by did not generated expected message.")

    checkEquals(obs, exp, message)
}

###########################################################
## calculateSignificantLevel() function
###########################################################

test.calculateSignificantLevel_true <- function() {

    filesDir <- system.file("extdata", "TEST", package="methylInheritance")

    results <- loadAllRDSResults(analysisResultsDir = filesDir,
                      permutationResultsDir = filesDir, doingSites = TRUE,
                      doingTiles = FALSE)

    iAll <- extractInfo(results, type = "sites", inter = "iAll", 1)

    obs <- methylInheritance:::calculateSignificantLevel(iAll)

    message <- paste0("test.calculateSignificantLevel_true() ",
                      "- Function did not return expected values")

    exp <- list(HYPER=1.0, HYPO=(2.0/4.0))

    checkEquals(obs, exp, msg = message)
}

###########################################################
## readInterGenerationResults() function
###########################################################

test.readInterGenerationResults_good_01 <- function() {

    filesDir <- system.file("extdata", "TEST", package="methylInheritance")

    ## Read DMS intergenerational results for the observed data
    obs <- methylInheritance:::readInterGenerationResults(outputDir =
            paste0(filesDir, "/"), 0, "sites")

    message <- paste0("test.readInterGenerationResults_good_01() ",
                      "- Function did not return expected values")

    iAll_1 <- GenomicRanges::GRanges(seqnames = rep("S", 4),
                           ranges = IRanges::IRanges(start = c(30222185, 15048832, 22963194, 23499048),
                                                     end = c(30222185, 15048832, 22963194, 23499048)),
                           strand = rep("+", 4),
                           typeDiff = c(1, rep(-1, 3)))

    i2_2 <- GenomicRanges::GRanges(seqnames = rep("S", 22),
                                   ranges = IRanges::IRanges(start = c(97481, 572272, 3281006, 11121503, 19260516,
                                                                       19445653, 22874019, 27232572, 30222185, 35929511,
                                                                       6085769,  8045209, 10355001, 11147625, 15048832,
                                                                       15438496, 22745004, 22899924, 22963194, 23499048,
                                                                       28622167, 34611139),
                                                             end = c(97481, 572272, 3281006, 11121503, 19260516,
                                                                     19445653, 22874019, 27232572, 30222185, 35929511,
                                                                     6085769,  8045209, 10355001, 11147625, 15048832,
                                                                     15438496, 22745004, 22899924, 22963194, 23499048,
                                                                     28622167, 34611139)),
                                   strand = rep("+", 22),
                                   typeDiff = c(rep(1, 10), rep(-1, 12)))

    i2_1 <- GenomicRanges::GRanges(seqnames = rep("S", 36),
                                   ranges = IRanges::IRanges(start = c(570115, 2573229, 5063112, 8247138, 8765627, 8791494,
                                                                       9955639, 11667875, 19095767, 26225126, 26798489, 27089337,
                                                                       27188724, 27236909, 27421271, 30222185, 30786437, 31364173,
                                                                       31396094, 33611091, 33886929,  3139258, 14391040, 15048832,
                                                                       15438613, 16630377, 17795264, 18396852, 22963194, 23499048,
                                                                       23499106, 23499111, 27019812, 30204193, 30746773, 35827911),
                                                             end = c(570115, 2573229, 5063112, 8247138, 8765627, 8791494,
                                                                     9955639, 11667875, 19095767, 26225126, 26798489, 27089337,
                                                                     27188724, 27236909, 27421271, 30222185, 30786437, 31364173,
                                                                     31396094, 33611091, 33886929,  3139258, 14391040, 15048832,
                                                                     15438613, 16630377, 17795264, 18396852, 22963194, 23499048,
                                                                     23499106, 23499111, 27019812, 30204193, 30746773, 35827911)),
                                   strand = rep("+", 36),
                                   typeDiff = c(rep(1, 21), rep(-1, 15)))

    exp <- list("i2" = list(i2_1, i2_2), "iAll" = list(iAll_1))

    checkEquals(as.data.frame(i2_1), as.data.frame(exp$i2[[1]]), msg = message)
    checkEquals(as.data.frame(i2_2), as.data.frame(exp$i2[[2]]), msg = message)
    checkEquals(as.data.frame(iAll_1), as.data.frame(exp$iAll[[1]]), msg = message)
}

test.readInterGenerationResults_good_02 <- function() {

    filesDir <- system.file("extdata", "TEST", package="methylInheritance")

    ## Read DMS intergenerational results for the observed data
    obs <- methylInheritance:::readInterGenerationResults(outputDir =
                                                              paste0(filesDir, "/"), 1, "sites")

    message <- paste0("test.readInterGenerationResults_good_02() ",
                      "- Function did not return expected values")

    iAll_1 <- GenomicRanges::GRanges(seqnames = rep("S", 5),
                                     ranges = IRanges::IRanges(start = c(17191066, 17424070, 1130005, 22786110, 26615081),
                                                               end = c(17191066, 17424070, 1130005, 22786110, 26615081)),
                                     strand = rep("+", 5),
                                     typeDiff = c(1, 1, rep(-1, 3)))

    i2_2 <- GenomicRanges::GRanges(seqnames = rep("S", 18),
                                   ranges = IRanges::IRanges(start = c(5507460,  8045221, 17191066, 17424070, 32510128,
                                                                       32911751, 33071323,  1130005,  5826332,  8045207,
                                                                       17804285, 18396726, 19869520, 21672484, 22786110,
                                                                       26615081, 32216298, 32216478),
                                                             end = c(5507460,  8045221, 17191066, 17424070, 32510128,
                                                                     32911751, 33071323,  1130005,  5826332,  8045207,
                                                                     17804285, 18396726, 19869520, 21672484, 22786110,
                                                                     26615081, 32216298, 32216478)),
                                   strand = rep("+", 18),
                                   typeDiff = c(rep(1, 7), rep(-1, 11)))

    i2_1 <- GenomicRanges::GRanges(seqnames = rep("S", 15),
                                   ranges = IRanges::IRanges(start = c(3401344, 17191066, 17424070, 24135743,
                                                                       27019812,  1130005,  1345775,  2573229,
                                                                       6717075, 18926407, 19260516, 22786110,
                                                                       23655774, 26615081, 33278578),
                                                             end = c(3401344, 17191066, 17424070, 24135743,
                                                                     27019812,  1130005,  1345775,  2573229,
                                                                     6717075, 18926407, 19260516, 22786110,
                                                                     23655774, 26615081, 33278578)),
                                   strand = rep("+", 15),
                                   typeDiff = c(rep(1, 5), rep(-1, 10)))

    exp <- list("i2" = list(i2_1, i2_2), "iAll" = list(iAll_1))

    checkEquals(as.data.frame(i2_1), as.data.frame(exp$i2[[1]]), msg = message)
    checkEquals(as.data.frame(i2_2), as.data.frame(exp$i2[[2]]), msg = message)
    checkEquals(as.data.frame(iAll_1), as.data.frame(exp$iAll[[1]]), msg = message)
}


###########################################################
## formatInputMethylData() function
###########################################################

test.formatInputMethylData_good_01 <- function() {

    initGR_01 <- list()
    initGR_01[[1]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1005, 1011, 1017), end = c(1005, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(71, 90, 95),
                                                numCs = c(0, 1, 1), numTs = c(71, 89, 94)), sample.id = "F1_1_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')
    initGR_01[[2]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1006, 1011, 1017), end = c(1006, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(93, 92, 93),
                                                numCs = c(1, 4, 0), numTs = c(92, 88, 93)), sample.id = "F1_2_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')

    initGR_02 <- list()
    initGR_02[[1]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1007, 1011, 1017), end = c(1007, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(90, 85, 79),
                                                numCs = c(0, 0, 1), numTs = c(90, 85, 78)), sample.id = "F2_1_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')
    initGR_02[[2]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1008, 1011, 1017), end = c(1008, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(73, 93, 78),
                                                numCs = c(0, 2, 0), numTs = c(73, 91, 78)), sample.id = "F2_2_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')

    initGR_03 <- list()
    initGR_03[[1]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1009, 1011, 1017), end = c(1009, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(80, 73, 84),
                                                numCs = c(0, 0, 1), numTs = c(80, 73, 83)), sample.id = "F3_1_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')
    initGR_03[[2]] <- new("methylRaw", data.frame(chr = rep("S", 3),
                                                start = c(1010, 1011, 1017), end = c(1010, 1011, 1017),
                                                strand = strand(rep("+", 3)), coverage = c(77, 80, 94),
                                                numCs = c(0, 2, 2), numTs = c(77, 78, 92)), sample.id = "F3_2_C",
                        assembly = "RNOR_5.0", context = "Cpg", resolution = 'base')

    initGR <- list()
    initGR[[1]] <- new("methylRawList", initGR_01, treatment = c(0, 1))
    initGR[[2]] <- new("methylRawList", initGR_02, treatment = c(0, 1))
    initGR[[3]] <- new("methylRawList", initGR_03, treatment = c(0, 1))

    set.seed(20011)
    obs <- methylInheritance:::formatInputMethylData(initGR)

    expGR <- list()
    expGR[[1]] <- new("methylRawList", list(initGR_01[[1]], initGR_02[[2]]), treatment = c(0, 1))
    expGR[[2]] <- new("methylRawList", list(initGR_02[[1]], initGR_03[[2]]), treatment = c(0, 1))
    expGR[[3]] <- new("methylRawList", list(initGR_03[[1]], initGR_01[[2]]), treatment = c(0, 1))

    message <- paste0("test.formatInputMethylData_good_01() ",
                      "- Function did not return expected values")

    checkEquals(obs, expGR, message)
}


###########################################################
## getGRangesFromMethylDiff() function
###########################################################

test.getGRangesFromMethylDiff_good_01 <- function() {
    permutationResultsFile <- system.file("extdata",
        "permutationResultsForSites.RDS", package="methylInheritance")
    permutationResults <- readRDS(permutationResultsFile)

    obs <- methylInheritance:::getGRangesFromMethylDiff(methDiff =
                    permutationResults, pDiff = 25, qvalue = 0.01, type = "hypo")

    exp <- list()

    exp[[1]] <- GRanges(seqnames = rep("S", 6), ranges = IRanges(start = c(572272, 6716939, 19483992,
                                                                           20354283, 23499048, 27019812),
                                                               end = c(572272, 6716939, 19483992,
                                                                       20354283, 23499048, 27019812)),
                        strand = rep("+", 6), pvalue = c(1.700864635138675e-87, 2.441717480904409e-19, 1.137547548463320e-23,
                        3.990798096127081e-17, 4.624679250110592e-99, 6.715374380810998e-18),
                        qvalue = c(7.472078736898228e-84, 2.167014921949277e-17, 2.039741644645623e-21, 2.897851124421653e-15,
                        4.063341288403986e-95, 5.000229134166011e-16), meth.diff = c(-48.728813559322035, -27.774983021857786, -30.785123966942145,
                        -26.135536439702882, -65.164453701293070, -27.095834649261331))
    exp[[2]] <- GRanges(seqnames = rep("S", 3), ranges = IRanges(start = c(6062088, 15438613, 23499048),
                        end = c(6062088, 15438613, 23499048)), strand = rep("+", 3), pvalue = c(5.837011155738509e-61,1.461524438688262e-24, 1.704531588950500e-16),
                        qvalue = c(5.158856586917255e-57, 2.583443744168598e-21, 1.004330673198592e-13), meth.diff = c(-51.405910822430378,-26.548592462963523,-26.087583898151358))
    exp[[3]] <- GRanges(seqnames = rep("S", 9), ranges = IRanges(start = c(97473, 461573, 4835309, 5063112, 8045209, 15438496, 20354375, 23499048, 26267942),
                        end = c(97473, 461573, 4835309, 5063112, 8045209, 15438496, 20354375, 23499048, 26267942)), strand = rep("+", 9),
                        pvalue = c(2.070118737044828e-15, 4.845855842583129e-29, 1.181308273263934e-25, 1.176727417787188e-26,
                                   1.986425155223842e-16, 2.450256665272661e-22, 7.280660237109421e-24, 8.552173905506492e-20, 2.955455569819033e-18),
                        qvalue = c(6.777240956277343e-13, 8.654209054465339e-26, 1.506926608558130e-22, 1.751263589010490e-23, 7.095109356448416e-14,
                                   1.562825322679899e-19, 6.721662253713180e-21, 4.019294405074884e-17, 1.319536279207790e-15),
                        meth.diff = c(-25.590676883780329, -25.456545654565453, -32.198928401110869, -29.107876406501159,
                                      -25.914367976223641, -27.358002274000036, -25.744386969983502, -27.730954849876422, -26.962446694888165))

    message <- paste0("test.getGRangesFromMethylDiff_good_01() ",
                      "- Function did not return expected values")

    checkEquals(obs, exp)
}


###########################################################
## interGeneration() function
###########################################################

test.interGeneration_good_01 <- function() {
    permutationResultsFile <- system.file("extdata", "permutationResultsForSites.RDS", package="methylInheritance")
    permutationResults <- readRDS(permutationResultsFile)

    resultsGR <- methylInheritance:::getGRangesFromMethylDiff(methDiff = permutationResults, pDiff = 10,
                                                    qvalue = 0.01, type = "hypo")

    obs <- methylInheritance:::interGeneration(resultsGR)

    exp <- list()
    exp[["i2"]] <- list()
    exp[["iAll"]] <- list()

    exp[["i2"]][[1]] <- GRanges(seqnames = rep("S", 15), ranges = IRanges(start = c(3139258, 14391040, 15048832, 15438613, 16630377,
                                                                               17795264, 18396852, 22963194, 23499048, 23499106,
                                                                               23499111, 27019812, 30204193, 30746773, 35827911),
                                                                end = c(3139258, 14391040, 15048832, 15438613, 16630377,
                                                                         17795264, 18396852, 22963194, 23499048, 23499106,
                                                                         23499111, 27019812, 30204193, 30746773, 35827911)),
                        strand = rep("+", 15), typeDiff = rep(-1, 15))

    exp[["i2"]][[2]] <- GRanges(seqnames = rep("S", 12), ranges = IRanges(start = c(6085769, 8045209, 10355001, 11147625,
                                                                                    15048832, 15438496, 22745004, 22899924,
                                                                                    22963194, 23499048, 28622167, 34611139),
                                                    end = c(6085769, 8045209, 10355001, 11147625,
                                                            15048832, 15438496, 22745004, 22899924,
                                                            22963194, 23499048, 28622167, 34611139)), strand = rep("+", 12), typeDiff = rep(-1, 12))

    exp[["iAll"]][[1]] <- GRanges(seqnames = rep("S", 3), ranges = IRanges(start = c(15048832, 22963194, 23499048),
                                                                 end = c(15048832, 22963194, 23499048)),
                                                            strand = rep("+", 3), typeDiff = rep(-1, 3))


    message <- paste0("test.interGeneration_good_01() ",
                      "- Function did not return expected values")

    checkEquals(obs, exp)
}


test.interGeneration_good_02 <- function() {
    permutationResultsFile <- system.file("extdata", "permutationResultsForSites.RDS", package="methylInheritance")
    permutationResults <- readRDS(permutationResultsFile)

    resultsGR <- methylInheritance:::getGRangesFromMethylDiff(methDiff = permutationResults, pDiff = 11,
                                                              qvalue = 0.01, type = "hyper")

    obs <- methylInheritance:::interGeneration(resultsGR)

    exp <- list()
    exp[["i2"]] <- list()
    exp[["iAll"]] <- list()

    exp[["i2"]][[1]] <- GRanges(seqnames = rep("S", 14), ranges = IRanges(start = c(570115, 2573229, 5063112, 8247138, 8791494,
                                                                                    9955639, 26798489, 27089337, 27188724, 27236909,
                                                                                    30222185, 30786437, 33611091, 33886929),
                                                                          end = c(570115, 2573229, 5063112, 8247138, 8791494,
                                                                                  9955639, 26798489, 27089337, 27188724, 27236909,
                                                                                  30222185, 30786437, 33611091, 33886929)),
                                strand = rep("+", 14), typeDiff = rep(1, 14))

    exp[["i2"]][[2]] <- GRanges(seqnames = rep("S", 10), ranges = IRanges(start = c(97481, 572272, 3281006, 11121503, 19260516,
                                                                                    19445653, 22874019, 27232572, 30222185, 35929511),
                                                                          end = c(97481, 572272, 3281006, 11121503, 19260516,
                                                                                  19445653, 22874019, 27232572, 30222185, 35929511)),
                                strand = rep("+", 10), typeDiff = rep(1, 10))

    exp[["iAll"]][[1]] <- GRanges(seqnames = rep("S", 1), ranges = IRanges(start = c(30222185),
                                                                           end = c(30222185)),
                                  strand = rep("+", 1), typeDiff = rep(1, 1))


    message <- paste0("test.interGeneration_good_02() ",
                      "- Function did not return expected values")

    checkEquals(obs, exp)
}