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Update package to version 1.15.1
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‎DESCRIPTION‎

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@@ -1,17 +1,17 @@
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Package: methylInheritance
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Version: 1.15.0
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Date: 2016-10-25
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Version: 1.15.1
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Date: 2021-04-06
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Title: Permutation-Based Analysis associating Conserved Differentially
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Methylated Elements Across Multiple Generations to a Treatment Effect
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Description: Permutation analysis, based on Monte Carlo sampling, for
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testing the hypothesis that the number of conserved
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differentially methylated elements, between several
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generations, is associated to an effect inherited from a
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treatment and that stochastic effect can be dismissed.
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Author: Astrid Deschênes, Pascal Belleau and Arnaud Droit
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Author@R: c(person("Astrid", "Deschênes", email="adeschen@hotmail.com",
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role=c("cre","aut")), person("Pascal", "Belleau",
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email="pascal.belleau@crchuq.ulaval.ca", role=c("aut")),
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Authors@R: c(person("Astrid", "Deschênes", email="adeschen@hotmail.com",
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role=c("cre","aut"), comment = c(ORCID = "0000-0001-7846-6749")),
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person("Pascal", "Belleau", email="pascal_belleau@hotmail.com",
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role=c("aut"), comment = c(ORCID = "0000-0002-0802-1071")),
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person("Arnaud", "Droit",
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email="arnaud.droit@crchuq.ulaval.ca", role=c("aut")))
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Depends: R (>= 3.5)
@@ -26,5 +26,4 @@ VignetteBuilder: knitr
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biocViews: BiologicalQuestion, Epigenetics, DNAMethylation,
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DifferentialMethylation, MethylSeq, Software, ImmunoOncology,
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StatisticalMethod, WholeGenome, Sequencing
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Maintainer: Astrid Deschenes <adeschen@hotmail.com>
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RoxygenNote: 7.1.1

‎NAMESPACE‎

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@@ -39,6 +39,7 @@ importFrom(ggplot2,xlab)
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importFrom(ggplot2,ylab)
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importFrom(gridExtra,grid.arrange)
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importFrom(gridExtra,tableGrob)
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importFrom(methods,is)
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importFrom(methods,new)
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importFrom(methylKit,calculateDiffMeth)
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importFrom(methylKit,filterByCoverage)

‎R/methylInheritanceInternalMethods.R‎

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@@ -285,6 +285,7 @@ validateRunPermutation <- function(methylKitData,
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#'
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#' @author Astrid Deschenes
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#' @importFrom S4Vectors isSingleInteger isSingleNumber
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#' @importFrom methods is
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#' @keywords internal
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validateRunObservation <- function(methylKitData,
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type, outputDir,
@@ -305,7 +306,7 @@ validateRunObservation <- function(methylKitData,
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}
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## Validate that methylKitData is a list of methylRawList
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if (class(methylKitData) != "list" ||
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if (!is(methylKitData, "list") ||
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!all(sapply(methylKitData, class) == "methylRawList")) {
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stop(paste0("methylKitData must be a list containing ",
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"\"methylRawList\" entries; each entry must contain ",
@@ -443,14 +444,15 @@ validateRunObservation <- function(methylKitData,
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#'
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#' @author Astrid Deschenes
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#' @importFrom S4Vectors isSingleInteger isSingleNumber
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#' @importFrom methods is
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#' @keywords internal
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validateExtractInfo <- function(allResults, type, inter, position) {
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if (!is.numeric(position) || floor(position) != position || position < 1) {
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stop("position must be a positive integer")
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}
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453-
if (!"methylInheritanceAllResults" %in% class(allResults)) {
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if (!is(allResults, "methylInheritanceAllResults")) {
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stop("allResults must be of class \"methylInheritanceAllResults\"")
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}
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‎inst/NEWS‎

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CHANGES IN VERSION 1.15.1
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------------------------
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BUG FIXES AND IMPROVEMENTS
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o Fix bug causing problem when using loadConvergenceData() with a different directory for the observation file and the permutation files.
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CHANGES IN VERSION 1.5.1
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------------------------
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SIGNIFICANT USER-VISIBLE CHANGES
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o New citation referring to the associated published article in Nucleic Acids Research.
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CHANGES IN VERSION 1.1.1
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------------------------
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‎inst/unitTests/test_methylInheritanceMethods.R‎

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###################################################
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METHYL_OBJ_FILE_01 <- system.file("extdata", "methylObj_001.RDS",
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package = "methylInheritance")
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package="methylInheritance")
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METHYL_OBJ_01 <- readRDS(METHYL_OBJ_FILE_01)
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15-
TEST_DIR <- system.file("extdata", "TEST", package = "methylInheritance")
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TEST_DIR <- system.file("extdata", "TEST", package="methylInheritance")
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data("methylInheritanceResults")
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@@ -41,15 +41,15 @@ test.runPermutation_methylKitData_not_valid_RDS <- function() {
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message <- paste0(" test.runPermutation_methylKitData_not_valid_RDS() ",
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"- Not valid file for methylKitData did not generated expected message.")
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44-
checkEquals(obs, exp, msg = message)
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checkEquals(obs, exp, msg=message)
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}
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## Test when all parameters valid
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test.runPermutation_good_001 <- function() {
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5050
if (!dir.exists("test_002")) {
51-
dir.create("test_002/SITES/", recursive = TRUE)
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dir.create("test_002/TILES/", recursive = TRUE)
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dir.create("test_002/SITES/", recursive=TRUE)
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dir.create("test_002/TILES/", recursive=TRUE)
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}
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obs <- runPermutation(methylKitData = METHYL_OBJ_FILE_01, runObservationAnalysis = FALSE,
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message <- paste0(" test.runObservation_methylKitData_not_valid() ",
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"- Not valid file for methylKitData did not generated expected message.")
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122-
checkEquals(obs, exp, msg = message)
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checkEquals(obs, exp, msg=message)
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}
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## Test when all parameters valid
126126
test.runObservation_good_001 <- function() {
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128128
if (!dir.exists("test_002")) {
129-
dir.create("test_002/SITES/", recursive = TRUE)
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dir.create("test_002/SITES/", recursive=TRUE)
130130
}
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obs <- runObservation(
133-
methylKitData = METHYL_OBJ_FILE_01, type = "sites",
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outputDir = "test_002", nbrCoresDiffMeth = 1,
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minReads = 10, minMethDiff = 5, qvalue = 0.05,
136-
maxPercReads = 99.9, destrand = FALSE, minCovBasesForTiles = 2,
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tileSize = 1000, stepSize = 100, vSeed = 200, saveInfoByGeneration = FALSE)
133+
methylKitData=METHYL_OBJ_FILE_01, type="sites",
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outputDir="test_002", nbrCoresDiffMeth=1,
135+
minReads=10, minMethDiff=5, qvalue = 0.05,
136+
maxPercReads=99.9, destrand=FALSE, minCovBasesForTiles=2,
137+
tileSize=1000, stepSize=100, vSeed=200,
138+
saveInfoByGeneration=FALSE)
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139-
obsV <- methylInheritance::loadAllRDSResults(permutationResultsDir = NULL,
140-
analysisResultsDir = "test_002")
140+
obsV <- methylInheritance::loadAllRDSResults(permutationResultsDir=NULL,
141+
analysisResultsDir="test_002")
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142143
exp <- list()
143144
exp[["OBSERVATION"]] <- list()
@@ -152,8 +153,8 @@ test.runObservation_good_001 <- function() {
152153
message <- paste0(" test.runObservation_good_001() ",
153154
"- All valid parameters did not generated expected result.")
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155-
checkEquals(obs, 0, msg = message)
156-
checkEquals(obsV$OBSERVATION, exp$OBSERVATION, msg = message)
156+
checkEquals(obs, 0, msg=message)
157+
checkEquals(obsV$OBSERVATION, exp$OBSERVATION, msg=message)
157158
}
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159160

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176177
message <- paste0(" test.extractInfo_good_01() ",
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"- Valid parameters for formatForGraph did not generated expected results.")
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179-
checkEquals(obs, exp, msg = message)
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checkEquals(obs, exp, msg=message)
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}
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182183

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231232
"- Valid parameters for loadAllRDSResults() ",
232233
"did not generated expected results.")
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234-
checkEquals(obs, exp, msg = message)
235+
checkEquals(obs, exp, msg=message)
235236
}
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237238

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270271
message <- paste0(" test.mergePermutationAndObservation_permutation_not_list() ",
271272
"- Not a list for permutationResults did not generated expected results.")
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273-
checkEquals(obs, exp, msg = message)
274+
checkEquals(obs, exp, msg=message)
274275
}
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276277
## Test result when all parameters are good
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322323
"- Valid parameters for mergePermutationAndObservation() ",
323324
"did not generated expected results.")
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325-
checkEquals(obs, exp, msg = message)
326+
checkEquals(obs, exp, msg=message)
326327
}
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328329
###########################################################
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340341
message <- paste0(" test.plotGraph_good_01() ",
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"- Valid parameters for plotGraph did not generated expected results.")
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343-
checkTrue("gtable" %in% class(obs), msg = message)
344-
checkEquals(class(obs[[1]]), "list", msg = message)
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checkEquals(class(obs[[2]]), "data.frame", msg = message)
344+
checkTrue(is(obs, "gtable"), msg=message)
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checkTrue(is(obs[[1]], "list"), msg=message)
346+
checkTrue(is(obs[[2]], "data.frame"), msg=message)
346347
}
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348349

@@ -366,9 +367,9 @@ test.plotConvergenceGraph_good_01 <- function() {
366367
message <- paste0(" test.plotConvergenceGraph_good_01() ",
367368
"- Valid parameters for plotGraph did not generated expected results.")
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369-
checkTrue("ggplot" %in% class(obs), msg = message)
370-
checkTrue(is(obs[[1]], "data.frame"), msg = message)
371-
checkTrue(is(obs[[2]], "list"), msg = message)
370+
checkTrue(is(obs, "ggplot"), msg=message)
371+
checkTrue(is(obs[[1]], "data.frame"), msg=message)
372+
checkTrue(is(obs[[2]], "list"), msg=message)
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373374
}
374375

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396397
message <- paste0(" test.loadConvergenceData_good_01() ",
397398
"- Valid parameters for loadConvergenceData did not generated expected results.")
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399-
checkEquals(class(data), "data.frame", msg = message)
400+
checkTrue(is(data, "data.frame"), msg = message)
400401
checkEquals(data , expected, msg = message)
401402
}
402403

@@ -456,12 +457,14 @@ test.loadConvergenceData_two_different_directories_by_5 <- function() {
456457
expected <- data.frame(NBR_PERMUTATIONS=c(5,5,10,10),
457458
ELEMENT=rep("SITES", 4), ANALYSIS=rep("iAll", 4),
458459
POSITION=rep(1, 4), TYPE=rep(c("HYPER", "HYPO"), 2),
459-
SIGNIFICANT_LEVEL=c(0.83333333333333337034, 0.33333333333333331483,
460-
0.72727272727272729291, 0.27272727272727270709))
460+
SIGNIFICANT_LEVEL=c(0.83333333333333337034,
461+
0.33333333333333331483,
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0.72727272727272729291,
463+
0.27272727272727270709))
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462465
message <- paste0(" test.loadConvergenceData_two_different_directories() ",
463466
"- Using two different directories for observation and permutation with loadConvergenceData did not generated expected results.")
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465-
checkEquals(class(data), "data.frame", msg = message)
466-
checkEquals(data , expected, msg = message)
468+
checkTrue(is(data, "data.frame"), msg=message)
469+
checkEquals(data , expected, msg=message)
467470
}

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