mergePermutationAndObservation: Merge the permutation results with the observation results.

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

Description

Merge the permutation results with the observation results. The merging is only needed when permutation and observation have been processed separately. The returned value is a methylInheritanceAllResults object that can be used by the extractInfo function.

Usage

mergePermutationAndObservation(permutationResults, observationResults)

Arguments

permutationResults	a list with 1 entry called PERMUTATION. The PERMUTATION entry is a list with a number of entries corresponding to the number of permutations that have been processed. Each entry contains the result of one permutation.
observationResults	a list with 1 entry called OBSERVATION. The OBSERVATION entry is a list containing the result obtained with the observed dataset (not shuffled).

Value

a list of class methylInheritanceAllResults with 2 entries. The 2 entries are:

• PERMUTATION list with a number of entries corresponding to the number of permutations that have been processed. Each entry contains the result of one permutation.The elements in each entry are:

  • SITES Only present when a sites analysis has been achieved, a list containing:

    • 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 on 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 on the number of generations.

  • TILES Only present when a tiles analysis has been achieved, a list containing:

    • i2 a list containing:

      • HYPER a list of integer, 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; etc.

      • HYPO a list of integer, 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; etc.

    • iAll a list containing:

      • HYPER a list of integer, the number of conserved hyper differentially methylated positions 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 on the number of generations.

      • HYPO a list of integer, the number of conserved hypo differentially methylated positions 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 on the number of generations.

• OBSERVATION a list containing the result obtained with the observed dataset (not shuffled). The elements are:

  • SITES Only present when a sites analysis has been achieved, a list containing:

    • 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 on 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 on the number of generations.

  • TILES Only present when a tiles analysis has been achieved, a list containing:

    • i2 a list containing:

      • HYPER a list of integer, 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; etc.

      • HYPO a list of integer, 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; etc.

    • iAll a list containing:

      • HYPER a list of integer, the number of conserved hyper differentially methylated positions 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 on the number of generations.

      • HYPO a list of integer, the number of conserved hypo differentially methylated positions 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 on the number of generations.

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

## Create a observation result
observed <- list()
observed[["OBSERVATION"]] <- list()
observed[["OBSERVATION"]][["SITES"]] <- list()
observed[["OBSERVATION"]][["SITES"]][["i2"]] <- list(HYPER = list(11, 10),
    HYPO = list(13, 12))
observed[["OBSERVATION"]][["SITES"]][["iAll"]] <- list(HYPER = list(1),
    HYPO = list(3))

## Create a permutation result containing only 1 permutation result
## Real perumtations results would have more entries
permutated <- list()
permutated[["PERMUTATION"]] <- list()
permutated[["PERMUTATION"]][[1]] <- list()
permutated[["PERMUTATION"]][[1]][["SITES"]] <- list()
permutated[["PERMUTATION"]][[1]][["SITES"]][["i2"]] <- list(HYPER =
    list(11, 12), HYPO = list(8, 11))
permutated[["PERMUTATION"]][[1]][["SITES"]][["iAll"]] <- list(HYPER =
    list(0), HYPO = list(1))

## Merge permutation and observation results
mergePermutationAndObservation(permutationResults = permutated,
    observationResults = observed)

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