validateRunPermutation: Parameters validation for the 'runPermutation' function

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

Description

Validation of all parameters needed by the public runPermutation function.

Usage

validateRunPermutation(
  methylKitData,
  type,
  outputDir,
  runObservedAnalysis,
  nbrPermutations,
  nbrCores,
  nbrCoresDiffMeth,
  minReads,
  minMethDiff,
  qvalue,
  maxPercReads,
  destrand,
  minCovBasesForTiles,
  tileSize,
  stepSize,
  vSeed,
  restartCalculation,
  saveInfoByGeneration
)

Arguments

methylKitData	a list of methylRawList entries or the name of the RDS file containing the list. Each methylRawList entry must contain all the methylRaw entries related to one generation (first entry = first generation, second entry = second generation, etc..). The number of generations must correspond to the number of entries in the methylKitData. At least 2 generations must be present to do a permutation analysis. More information can be found in the methylKit package.
type	One of the "sites","tiles" or "both" strings. Specifies the type of differentially methylated elements should be returned. For retrieving differentially methylated bases type="sites"; for differentially methylated regions type="tiles". Default: "both".
outputDir	a string, the name of the directory that will contain the results of the permutation. If the directory does not exist, it will be created.
runObservedAnalysis	a logical, when runObservedAnalysis = TRUE, a CpG analysis on the observed dataset is done.
nbrPermutations,	a positive integer, the total number of permutations that is going to be done.
nbrCores	a positive integer, the number of cores to use when processing the analysis.
nbrCoresDiffMeth	a positive integer, the number of cores to use for parallel differential methylation calculations.Parameter used for both sites and tiles analysis. The parameter corresponds to the num.cores parameter in the methylKit package.
minReads	a positive integer Bases and regions having lower coverage than this count are discarded. The parameter corresponds to the lo.count parameter in the methylKit package.
minMethDiff	a positive double betwwen [0,100], the absolute value of methylation percentage change between cases and controls. The parameter corresponds to the difference parameter in the methylKit package.
qvalue	a positive double betwwen [0,1], the cutoff for qvalue of differential methylation statistic. TODO
maxPercReads	a double between [0,100], the percentile of read counts that is going to be used as upper cutoff. Bases ore regions having higher coverage than this percentile are discarded. Parameter used for both CpG sites and tiles analysis. The parameter correspond to the hi.perc parameter in the methylKit package.
destrand	a logical, when TRUE will merge reads on both strands of a CpG dinucleotide to provide better coverage. Only advised when looking at CpG methylation. Parameter used for both CpG sites and tiles analysis.
minCovBasesForTiles	a non-negative integer, the minimum number of bases to be covered in a given tiling window. The parameter corresponds to the cov.bases parameter in the package methylKit. Only used when doingTiles = TRUE. Default: 0.
tileSize	a positive integer, the size of the tiling window. The parameter corresponds to the win.size parameter in the methylKit package. Only used when doingTiles = TRUE.
stepSize	a positive integer, the step size of tiling windows. The parameter corresponds to the stepSize parameter in the methylKit package. Only used when doingTiles = TRUE.
vSeed	a integer, a seed used when reproducible results are needed. When a value inferior or equal to zero is given, a random integer is used.
restartCalculation	a logical, when TRUE, only permutations that don't have an associated RDS result file are run. Useful to restart a permutation analysis that has been interrupted.
saveInfoByGeneration	a logical, when TRUE, the information about differentially methylated sites and tiles for each generation is saved in a RDS file. The information is saved in a different file for each permutation. The files are only saved when the outputDir is not NULL.

Value

0 indicating that all parameters validations have been successful.

Author(s)

Astrid Deschenes

Examples

## Load dataset
data(samplesForTransgenerationalAnalysis)

## The function returns 0 when all paramaters are valid
methylInheritance:::validateRunPermutation(
    methylKitData = samplesForTransgenerationalAnalysis, type = "sites",
    outputDir = "test", runObservedAnalysis = TRUE,
    nbrPermutations = 10000, nbrCores = 1,
    nbrCoresDiffMeth = 1, minReads = 10, minMethDiff = 25, qvalue = 0.01,
    maxPercReads = 99.9, destrand = TRUE, minCovBasesForTiles = 10,
    tileSize = 1000, stepSize = 500, vSeed = 12, restartCalculation = FALSE,
    saveInfoByGeneration = FALSE)

## The function raises an error when at least one paramater is not valid
## Not run: methylInheritance:::validateRunPermutation(
    methylKitData = "HI", type = "tiles", outputDir = "test",
    runObservedAnalysis = FALSE, nbrPermutations = 10000, nbrCores = 1,
    nbrCoresDiffMeth = 1, minReads = 10, minMethDiff = 25, qvalue = 0.01,
    maxPercReads = 99.9, destrand = TRUE, minCovBasesForTiles = 10,
    tileSize = 1000, stepSize = 500, vSeed = 12, restartCalculation = FALSE,
    saveInfoByGeneration = FALSE)
## End(Not run)

adeschen/methylInheritance documentation built on April 21, 2021, 9:45 a.m.