interGeneration: Calculate the intersection of the differentially methylated...

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

Description

Calculate the intersection of the differentially methylated results for two or more consercutive generations using a list of GRanges where each entry represents the results for one generation.

Usage

interGeneration(resultAllGenGR)

Arguments

resultAllGenGR

a list of GRanges as created by the getGRangesFromMethylDiff function. Each entry of the list represents the differentially methylated results for one generation (first entry = first genertation, second entry = second generation, etc..). Each GRanges object holds statistics for differentially methylated regions/bases.

Value

a list containing the following elements:

• i2 a list of GRanges Each GRanges represents the intersection of analysis results between two consecutive generations. The first element represents the intersection of the first and second generations; the second element, the intersection of the second and third generations; etc.. The number of entries depends of the number of generations.

• iAll a list of GRanges. Each GRanges represents the intersection fo the analysis results between three or more consecutive generations. The first element represents the intersection of the first three generations; the second element, the intersection of the first fourth generations; etc..The number of entries depends of the number of generations.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Load permutation results on sites
permutationResultsFile <- system.file("extdata",
    "permutationResultsForSites.RDS", package="methylInheritance")
permutationResults <- readRDS(permutationResultsFile)

## Transform result to GRanges
resultsGR <- methylInheritance:::getGRangesFromMethylDiff(methDiff =
    permutationResults, pDiff = 10, qvalue = 0.01, type = "hyper")

## Extract inter generational conserved sites
conservedSitesGR <- methylInheritance:::interGeneration(resultsGR)

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