demoForTransgenerationalAnalysis: The methylation information from samples over three...

In methylInheritance: Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

Description

The object is a list with 3 entries. Each entry corresponds to the information for one generation (first entry = first generation, etc..) stored in a methylRawList object. There are 12 samples (6 controls and 6 cases) for each generation. Each sample information is stored in a methylRaw object.

Usage

data(demoForTransgenerationalAnalysis)

Format

A list containing three methylRawList objects. Each methylRawList contains the information for one generation (first entry = first generation, etc..). Each sample information is stored in a methylRaw object. There is methylRaw objects (6 controls and 6 cases) in each generation.

Details

This dataset can be used to test runPermutation and runObservation functions.

Value

A list containing three methylRawList objects. Each methylRawList contains the information for one generation (first entry = first generation, etc..). Each sample information is stored in a methylRaw object. There is methylRaw objects (6 controls and 6 cases) in each generation.

See Also

• runPermutation for running a permutation analysis, and optionally an observation analysis, using multi-generational dataset

• runObservation for running an observation analysis using methylKit info entry

Examples

## Loading dataset
data(demoForTransgenerationalAnalysis)

## Run a permutation analysis
runObservation(methylKitData = demoForTransgenerationalAnalysis,
    outputDir = "test_demo", type = "tiles", vSeed = 2001)

## Get results
result <- loadAllRDSResults(analysisResultsDir = "test_demo",
    permutationResultsDir = NULL, doingSites = FALSE,
    doingTiles = TRUE)

## Remove result directory
if (dir.exists("test_demo")) {
    unlink("test_demo", recursive = TRUE)
}

methylInheritance documentation built on Nov. 8, 2020, 8:21 p.m.