samplesForChrSynthetic: All samples information, formated by 'methylKit', in a...
In methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description Usage Format Details Value See Also Examples

The object is a methylBase. There is 12 samples (6 controls and 6 cases). Each sample information is stored in a methylRaw object.

1	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)
}