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)

[Package methylInheritance version 1.6.1 Index]