validateRunSimLogicalParameters: Parameters validation for the 'runSim' function. Only logical...
In methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description Usage Arguments Value Author(s) Examples

View source: R/methylInheritanceSimInternalMethods.R

Validation of all parameters needed by the public runSim function. Only logical parameters are validated.

1 2	validateRunSimLogicalParameters(keepDiff, saveGRanges, saveMethylKit, runAnalysis)

`keepDiff`	`logical` if true, the differentially methyled sites will be the same for each parameter (`vpDiff`, `vDiff` and `vInheritance`). Default: `FALSE`.
`saveGRanges`	a `logical`, when `true`, the package save two files type. The first generate for each simulation contains a `list`. The length of the `list` corresponds to the number of generation. The generation are stored in order (first entry = first generation, second entry = second generation, etc..). All samples related to one generations are contained in a `GRangesList`. The `GRangeaList` store a `list` of `GRanges`. Each `GRanges` stores the raw mehylation data of one sample. The second file a numeric `vector` denoting controls and cases (a file is generates by entry in the `vector` parameters `vNbSample`).
`saveMethylKit`	a `logical`, when `TRUE`, for each simulations save a file contains a `list`. The length of the `list` corresponds to the number of generation. The generation are stored in order (first entry = first generation, second entry = second generation, etc..). All samples related to one generations are contained in a S4 `methylRawList` object. The `methylRawList` object contains two Slots: 1. treatment: A numeric `vector` denoting controls and cases. 2. .Data: A `list` of `methylRaw` objects. Each object stores the raw methylation data of one sample.
`runAnalysis`	a `logical`, if `TRUE`, two files are saved for each simulation: 1. The first file is the methylObj... file formated with the `methylkit` package in a S4 `methylBase` object (with the `methylKit` functions: `filterByCoverage`, `normalizeCoverage` and `unite`). 2. The second file contains a S4 `calculateDiffMeth` object generated with the `methylKit` functions `calculateDiffMeth` on the first file.

0 indicating that the function has been successful.

Pascal Belleau, Astrid Deschenes

## Load dataset
data("samplesForChrSynthetic")

## The function returns 0 when all paramaters are valid
methInheritSim:::validateRunSimLogicalParameters(keepDiff = FALSE, 
saveGRanges = TRUE, saveMethylKit = FALSE, runAnalysis = FALSE)