interGeneration {methylInheritance}

R Documentation

Calculate the intersection of the differentially methylated results for two or more consercutive generations

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)

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