samplesForChrSynthetic {methInheritSim} | R Documentation |
methylKit
, in a
methylBase
format (for demo purpose).The object is a methylBase
.
There is 12 samples (6 controls and 6 cases). Each
sample information is stored in a methylRaw
object.
data(samplesForChrSynthetic)
A methylBase
object contains the information for one
generation. Each sample information is
stored in a methylRaw
object. There is methylRaw
objects
(6 controls and 6 cases).
This dataset can be
used to test the runSim
function.
A methylBase
contains the information for one generation.
Each sample information is stored in a methylRaw
object.
There is methylRaw
objects
(6 controls and 6 cases).
runSim
for running a
simulation analysis using methylKit info as input
## Loading dataset data(samplesForChrSynthetic) ## Set the output directory where files will be created temp_dir <- "test_samplesForChrSynthetic" ## Create 4 simulated dataset (nbSimulation) ## over 3 generations (nbGenration = 3) with ## 6 cases and 6 controls (nNbsample = 6) using only one set ## of parameters (vpDiff = 0.85, vpDiffsd = 0.1, vDiff = 0.8) runSim(outputDir = temp_dir, fileID = "F1", nbSynCHR = 1, methData = samplesForChrSynthetic, nbSimulation = 4, nbBlock = 10, nbCpG = 20, nbGeneration = 3, vNbSample = c(6), vpDiff = c(0.85), vpDiffsd = c(0.1), vDiff = c(0.8), vInheritance = c(0.5), propInherite = 0.3, rateDiff = 0.3, minRate = 0.2, propHetero = 0.5, nbCores = 1, vSeed = 32) ## Delete the output directory and its content if (dir.exists(temp_dir)) { unlink(temp_dir, recursive = TRUE, force = FALSE) }