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 nonnegative 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 nonnegative 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 nonnegative 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.
