createDataStructure {methylInheritance} | R Documentation

## Extract the number of conserved differentially methylated elements in `GRanges`.

### Description

Extract the number of conserved differentially methylated elements in `GRanges`. Each `GRanges` is the result of one intersection between two or more consecutive generations for one analysis done on all generations. The hypo and hyper differentially methylated elements are counted separatly.

### Usage

    createDataStructure(interGenerationGR)

### Arguments

`interGenerationGR` | a `list` that contains the information for all differentially methylated analysis done on each generation present in the initial dataset. The `list` must contain 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.

### Value

a `list` containing the following elements:

- `i2` a `list` containing:

  - `HYPER` a `list` of `integer`, the number of conserved hyper differentially methylated sites 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..

  - `HYPO` a `list` of `integer`, the number of conserved hypo differentially methylated sites 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..

- `iAll` a `list` containing:

  - `HYPER` a `list` of `integer`, the number of conserved hyper differentially methylated sites 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.

  - `HYPO` a `list` of `integer`, the number of conserved hypo differentially methylated sites 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)

Astrid Deschenes, Pascal Belleau

### Examples

    ## Get the name of the directory where the file is stored
    filesDir <- system.file("extdata", "TEST", package="methylInheritance")

    ## Load file containing results from a observation analysis
    obsResults <- readRDS(file = paste0(filesDir,
        "/SITES/SITES_observed_results.RDS"))

    ## Create data structure using information form the observation analysis
    formatedResults <- methylInheritance:::createDataStructure(obsResults)

[Package methylInheritance version 1.11.0 Index]