validateRunSimLogicalParameters {methInheritSim} | R Documentation |
Parameters validation for the runSim
function. Only
logical parameters are validated.
Description
Validation of all parameters needed by the public
runSim
function. Only logical parameters are validated.
Usage
validateRunSimLogicalParameters(keepDiff, saveGRanges, saveMethylKit,
runAnalysis)
Arguments
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.
|
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:::validateRunSimLogicalParameters(keepDiff = FALSE,
saveGRanges = TRUE, saveMethylKit = FALSE, runAnalysis = FALSE)
[Package
methInheritSim version 1.16.0
Index]