validateRunSimParameters: Parameters validation for the 'runSim' function.

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

Description

Validation of all parameters needed by the public runSim function.

Usage

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)

Arguments

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.

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:::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")

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