methylInheritanceResults {methylInheritance} | R Documentation

## All observed and permutation results formatted in a `methylInheritanceResults` class (for demo purpose).

### Description

The object is a `list` with 2 entries: "OBSERVATION" and "PERMUTATION".

### Usage

    data(methylInheritanceResults)

### Format

a `list` of class `methylInheritanceAllResults` containing the following elements:

- `OBSERVATION` a `list` containing:

  - `SITES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, 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.

      - `HYPO` a `list` of `integer` with 2 entries, 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated sites between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated sites between the three consecutive generations.

  - `TILES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, the number of conserved hyper differentially methylated positions 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.

      - `HYPO` a `list` of `integer` with 2 entries, the number of conserved hypo differentially methylated positions 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated positions between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated positions between the three consecutive generations.

- `PERMUTATION` a `list` containing `nbrPermutations` entries. Each entry is a `list` containing:

  - `SITES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, 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.

      - `HYPO` a `list` of `integer` with 2 entries, 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated sites between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated sites between the three consecutive generations.

  - `TILES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, the number of conserved hyper differentially methylated positions 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.

      - `HYPO` a `list` of `integer` with 2 entries, the number of conserved hypo differentially methylated positions 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated positions between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated positions between the three consecutive generations.

### Details

This dataset can be used to test the `extractInfo` function.The extracted information can be used to calculate the significant level or to create a graph.

### Value

a `list` of class `methylInheritanceAllResults` containing the following elements:

- `OBSERVATION` a `list` containing:

  - `SITES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, 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.

      - `HYPO` a `list` of `integer` with 2 entries, 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated sites between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated sites between the three consecutive generations.

  - `TILES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, the number of conserved hyper differentially methylated positions 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.

      - `HYPO` a `list` of `integer` with 2 entries, the number of conserved hypo differentially methylated positions 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated positions between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated positions between the three consecutive generations.

- `PERMUTATION` a `list` containing a number of entries corresponding to the number of permutations that have been produced. Each entry is a `list` containing:

  - `SITES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, 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.

      - `HYPO` a `list` of `integer` with 2 entries, 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated sites between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated sites between the three consecutive generations.

  - `TILES` a `list` containing:

    - `i2` a `list` containing:

      - `HYPER` a `list` of `integer` with 2 entries, the number of conserved hyper differentially methylated positions 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.

      - `HYPO` a `list` of `integer` with 2 entries, the number of conserved hypo differentially methylated positions 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.

    - `iAll` a `list` containing:

      - `HYPER` a `list` of `integer` with 1 entry, the number of conserved hyper differentially methylated positions between the three consecutive generations.

      - `HYPO` a `list` of `integer` with 1 entry, the number of conserved hypo differentially methylated positions between the three consecutive generations.

### See Also

- `extractInfo` for extracting the information specific to a subsection of the permutation analysis

### Examples

    ## Loading dataset containing all results
    data(methylInheritanceResults)

    ## Extract information for the intersection between conserved differentially
    ## methylated sites (type = sites) between the intersection of 2
    ## generations (inter = i2): F1 and F2 (position = 1)
    extractInfo(allResults = methylInheritanceResults,
        type = "sites", inter="i2", 1)

[Package methylInheritance version 1.11.0 Index]