methData 
an object of class methylBase , the CpG information
from controls (CTRL) that will be used to create the synthetic chromosome.
The methData object can also contain information from cases but
only the controls are used.

nbSynCHR 
a positive integer , the number of distinct synthetic
chromosomes that will be generated.

nbSimulation 
a positive integer , the number of simulations
generated
for each parameter (vNbSample , vpDiff , vDiff and
vInheritance ).
The total number of simulation is
nbSimulation * length(vNbSample) * length(vpDiff) *
length(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 .

nbGeneration 
a positive integer , the number of generations
simulated.

vNbSample 
a vector of distinct positive integer ,
the number of controls (CTRL) and cases in the simulated dataset. In
the simulated dataset, the number of CTRL equals the number of cases.
The number of CTRL do not need to be equal to the number of Case in
the real methData dataset.

vpDiff 
a vector of distinct 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. Note that vpDiff and vpDiffsd
must be the same length.

vpDiffsd 
a vector of a nonnegative double , the
standard deviation associated to the vpDiff . Note that
vpDiff and vpDiffsd must be the same length.

vDiff 
a vector of distinct nonnegative double
included in [0,1], the proportion of C/T for a case differentially
methylated that follows
a beta distribution where the mean is shifted by vDiff
from the CTRL distribution.

vInheritance 
a vector of distinct nonnegative double
included in [0,1], the proportion of cases
that inherits differentially methylated sites.

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 for differentially methylated sites.

propInherite 
a nonnegative double inferior or equal
to 1 , the proportion of differentially methylated regions that
are inherated.

propHetero 
a nonnegative double between [0,1], the
reduction of vDiff for the second and following generations.

keepDiff 
a logical , when TRUE , the
differentially methylated sites
will be the same for all simulated datasets. Datasets generated using
differents parameter values from vector parameters (vpDiff ,
vDiff and vInheritance ) wil all have the same differentially
methylated sites.

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 a directory called "outputDir" that is located 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"

minReads 
a positive integer , sites and regions having lower
coverage than this count are discarded. The parameter
corresponds to the lo.count parameter in
the methylKit package.

maxPercReads 
a double between [0,100], the percentile of read
counts that is going to be used as upper cutoff. Sites and regions
having higher
coverage than maxPercReads are discarded. This parameter is used for
both CpG sites and tiles analysis. The parameter
correspond to the hi.perc parameter in the methylKit package.

meanCov 
a positive integer , the mean of the coverage
at the simulated CpG sites.

context 
a string of character , the short description of the
methylation context, such as "CpG", "CpH", "CHH", etc..

assembly 
a string of character , the short description of the
genome assembly, such as "mm9", "hg18", etc..

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 (using the methylKit
functions: filterByCoverage , normalizeCoverage and
unite ).
2. The second file contains a S4 calculateDiffMeth object
generated
using the methylKit functions calculateDiffMeth on the
first file.

nbCores 
a positive integer , the number of cores used 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. .
