validateRunSimLogicalParameters: Parameters validation for the 'runSim' function. Only logical...

In belleau/methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description

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

Usage

validateRunSimLogicalParameters(keepDiff, saveGRanges, saveMethylKit,
  runAnalysis)

Arguments

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.

Value

0 indicating that the function has been successful.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Load dataset
data("samplesForChrSynthetic")

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

belleau/methInheritSim documentation built on April 1, 2020, 2:43 p.m.