extractInfo {methylInheritance} | R Documentation

## Extract the information specific to a subsection of the permutation analysis

### 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)

[Package methylInheritance version 1.11.0 Index]