createDataStructure: Extract the number of conserved differentially methylated...

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

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)

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