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

Description Usage Arguments Value Author(s) Examples

View source: R/methylInheritanceSimInternalMethods.R

Description

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

Usage

1
2
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

1
2
3
4
5
6
## 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.