validateRunSimOtherParameters {methInheritSim} | R Documentation |
Parameters validation for the runSim
function. Only
parameters other than double, integer and logical are validated.
Description
Validation of all parameters needed by the public
runSim
function. Only parameters other than double, integer
and logical are validated.
Usage
validateRunSimOtherParameters(outputDir, fileID, methData, context, assembly)
Arguments
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:::validateRunSimOtherParameters(
outputDir = "test", fileID = "test", methData = samplesForChrSynthetic,
context = "CpG", assembly = "Rnor_5.0")
[Package
methInheritSim version 1.6.0
Index]