methylInheritanceResults: All observed and permutation results formatted in a...

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

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)

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