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Merge runPermutationUsingRDSFile() and runPermutationUsingMethylKitInfo() into 1 function called runPermutation()

Instead of dir(), use:

system.file("extdata", "resultsForTransgenerationalAnalysis.RDS",
package="methylInheritance")

Hi, I would like to use your package for the analysis of RRBS data. First of all, do you think it is appropiate to use Mathylinheritance with RRBS data or should it be only fro WGBS? Can or should I make any fine-tuning for RRBS? Also, once the conserved DMCs are identified, how can I know the actual positions of the conserved DMCs? I manage to extract the results of each permutation but not the chromosome, start, end of each CpG that is conserved. Finally, I would like to ask if I can use this package with only 2 generations instead of 3. Thank you very much for your help!

List of typos:

• a \code{list} of class \code{} when ...
• @return a \code{list} containing...
• itemize (instead of \itemize
  etc...

Remove \dontrun in examples section of the man pages

Use a try/catch strategy to remove all warnings generated by the methylKit functions. Use it for the specific warning: "glm.fit: fitted probabilities numerically 0 or 1 occurred". This warning is not related to a real problem.

Merge runObservationUsingRDSFile() and runObservationUsingMethylKitInfo() into 1 function called runObservation()

Indent code properly so it's easier to read/understand e.g.
runPermutationUsingMethylKitInfo(
samplesForTransgenerationalAnalysis,
type="sites", nbrPermutations=3, vSeed=221)
instead of
runPermutationUsingMethylKitInfo(methylKitInfo =
samplesForTransgenerationalAnalysis, type = "sites",
nbrPermutations = 3, vSeed = 221)

In vignette, change:
slot(demoForTransgenerationalAnalysis[[1]], "treatment")

to:
demoForTransgenerationalAnalysis[[1]]@treatment

Trying to load convergence data to get data.frame with p-values and then plot. However, I get an error stating: Error in seq.default(by, nbFiles, by) : wrong sign in 'by' argument

Currently to get seqFiles code (?):
filesInDir <- list.files(path = paste0(analysisResultsDir, toupper(type), "/"), pattern = "[[:digit:]].RDS", all.files = FALSE, full.names = TRUE, recursive = FALSE, ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)

nbFiles <- length(filesInDir)

seqFiles <- unique(c(seq(by, nbFiles, by), nbFiles))

I believe the code to get list.files should be :

list.files(path = paste0(permutationResultsDir, "/", toupper(type)), pattern ="[[:digit:]].RDS", all.files = FALSE,full.names = TRUE, recursive = FALSE,ignore.case = FALSE, include.dirs = FALSE, no.. = FALSE)

(since we are counting the number of permutations done, should be go to permutation folder (and not analysis). Placement of "/" in wrong positions, since directory for permuations is: Permu_folder/type/TYPE_permutation_1/RDS )

attempting to run the "corrected" list.files, returns a list of all the permuation files that were performed

Misspelled function names in the vignette: runPermutationUsingMehtylKitInfo() and runObservationUsingMehtylKitInfo()