extractInfo: Extract the information specific to a subsection of the...

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

Description

Extract the information specific to a subsection of the permutation analysis. The extracted information will be specific to one type of differential methylation analysis (tiles or sites), to one type of intersection (two consecutive generation or more) and to one specific group of generations.

Usage

extractInfo(allResults, type = c("sites", "tiles"), inter = c("i2",
  "iAll"), position = 1)

Arguments

allResults	a list of class methylInheritanceAllResults as created by the runPermutation function. The list must contain two entries : "PERMUTATION" and "OBSERVATION". The "PERMUTATION" list must contain all results from all permutations while the "OBSERVATION" list must contain the result obtained with the observed dataset (not shuffled).
type	One of the "sites" or "tiles" strings. Specifies the type of differentially methylated elements should be returned. For retrieving differentially methylated bases type = "sites"; for differentially methylated regions type = "tiles". Default: "sites".
inter	One of the "i2" or "iAll" strings. Specifies the type of intersection should be returned. For retrieving intersection results between two consecutive generations inter = "i2"; for intersection results between three generations or more inter = "iAll". Default: "i2".
position	a positive integer, the position in the list where the information will be extracted. Default=1.

Value

a data.frame containing the observation results (using real data) and the permutation results (using shuffled data). Both hyper and hypo differentially conserved methylation results are present.

Author(s)

Astrid Deschenes, Pascal Belleau

Examples

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

## Load information from files
results <- loadAllRDSResults(analysisResultsDir = filesDir,
    permutationResultsDir = filesDir, doingSites = TRUE, doingTiles = TRUE)

## 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)
info <- extractInfo(allResults = results, type = "sites", inter="i2", 1)

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