validateRunSimParameters: Parameters validation for the 'runSim' function.
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.

validateRunSimParameters(vpDiff, vpDiffsd, vDiff, vInheritance, propInherite,
  rateDiff, minRate, propHetero, maxPercReads, nbSynCHR, nbSimulation, nbBlock,
  nbCpG, vNbSample, nbGeneration, minReads, meanCov, nbCores, vSeed, keepDiff,
  saveGRanges, saveMethylKit, runAnalysis, outputDir, fileID, methData, context,
  assembly)

`vpDiff`	a `double` superior to `0` and inferior or equal to `1`, the mean value for the proportion of samples that will have, for a specific position, differentially methylated values. It can be interpreted as the penetrance.
`vpDiffsd`	a non-negative `double`, the standard deviation associated to the `propDiff`.
`vDiff`	a positive `double` between [0,1], the proportion of C/T for a case differentially methylated follow a beta distribution where the mean is shifted of `vDiff` from the CTRL distribution
`vInheritance`	a positive `double` between [0,1], the proportion of cases that inherited differentially sites.
`propInherite`	a non-negative `double` inferior or equal to `1`, the proportion of differentially methylated site are inherated
`rateDiff`	a positive `double` inferior to `1`, the mean of the chance that a site is differentially methylated.
`minRate`	a non-negative `double` inferior to `1`, the minimum rate of differentially methylated sites.
`propHetero`	a positive `double` between [0,1], the reduction of vDiff for the second and following generations.
`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.
`nbSynCHR`	a positive `integer`, the number of distinct synthetic chromosomes that will be generated.
`nbSimulation`	a positive `integer`, the number of simulations for each parameter (`vNbSample`, `vpDiff`, `vDiff` and `vInheritance`).
`nbBlock`	a positive `integer`, the number of blocks used for sampling.
`nbCpG`	a positive `integer`, the number of consecutive CpG positions used for sampling from `methInfo`.
`vNbSample`	a `vector` of positive `integer`, the number of methData (CTRL) and cases in the the simulation dataset. In the simulated dataset, the number of CTRL equals the number of Case. The number of CTRL do not need to be equal to the number of Case in the real dataset.
`nbGeneration`	a positive `integer`, the number of generations.
`minReads`	a positive `integer` Bases and regions having lower coverage than this count are discarded. The parameter correspond to the `lo.count` parameter in the `methylKit` package.
`meanCov`	a positive `integer` represent the mean of the coverage at the CpG site Default: `80`.
`nbCores`	a positive `integer`, the number of cores to use when creating the simulated datasets. Default: `1` and always `1` for Windows.
`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. Default: `-1`.
`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.
`outputDir`	a string of `character` or `NULL`, the path where the files created by the function will be saved. When `NULL`, the files are saved in the current directory.
`fileID`	a string of `character`, a identifiant that will be included in each output file name. Each output file name is composed of those elements, separated by "_": a type name, ex: methylGR, methylObj, etc.. a `fileID` the chromosome number, a number between 1 and `nbSynCHR` the number of samples, a number in the `vNbSample` `vector` the mean proportion of samples that has, for a specific position, differentially methylated values, a number in the `vpDiff` `vector` the proportion of C/T for a case differentially methylated that follows a shifted beta distribution, a number in the `vDiff` `vector` the proportion of cases that inherits differentially sites, a number in the `vInheritance` `vector` the identifiant for the simulation, a number between 1 and `nbSimulation` the file extension ".rds"
`methData`	an object of class `methylBase`, the CpG information from controls (CTRL) that will be used to create the sythetic chromosome. The `methData` object can also contain information from cases but only the controls will be used.
`context`	a string of `character`, the methylation context string, ex: CpG,CpH,CHH, etc.
`assembly`	a string of `character`, the short description of the genome assembly. Ex: mm9,hg18 etc.

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:::validateRunSimParameters(vpDiff =0.2, 
vpDiffsd = 0.3, vDiff = 0.4, vInheritance = 0.2, propInherite = 0.5, 
rateDiff = 0.2, minRate = 0.1, propHetero = 0.2, maxPercReads = 99.1, 
nbSynCHR = 1, nbSimulation = 2, nbBlock = 10, nbCpG = 4, vNbSample = 10, 
nbGeneration = 3, minReads = 10, meanCov = 80, 
nbCores = 1, vSeed = -1, keepDiff = FALSE, saveGRanges = TRUE, 
saveMethylKit = FALSE, runAnalysis = FALSE, outputDir = "test", 
fileID = "test", methData = samplesForChrSynthetic, 
context = "CpG", assembly = "Rnor_5.0")