getGRangesFromMethylDiff {methylInheritance} | R Documentation

## Transform results from a CpG site or region analysis done on mutliple generations into a `list` of `GRanges` objects

### Description

Transform a `list` of `methylDiff` objects into a `list` of `GRanges` objects. Each `methylDiff` object represent a CpG site or region analysis done on one generation.

### Usage

    getGRangesFromMethylDiff(
      methDiff,
      pDiff,
      qvalue,
      type = c("all", "hyper", "hypo")
    )

### Arguments

`methDiff` | a `list` of S4 `methylDiff` class objects, each entry of the `list` represents the differentially methylated results for one generation (first entry = first genertation, second entry = second generation, etc..). Each `methylDiff` object holds statistics and locations for differentially methylated regions/bases.
`pDiff` | a positive `double` between `0` and `100`, the cutoff for absolute value of methylation percentage change between test and control.
`qvalue` | a positive `double` inferior to `1`, the cutoff for qvalue of differential methylation statistic.
`type` | One of the `"hyper"`,`"hypo"` or `"all"` strings, the string specifies what type of differentially methylated bases/tiles should be treated For retrieving hyper-methylated tiles/sites `type` = `"hyper"`; for hypo-methylated `type` = `"hypo"`. Default: `"all"`.

### Value

a `list` of `GRanges` objects, each entry of the `list` represents the differentially methylated results for one generation (first entry = first genertation, second entry = second generation, etc..). Each `GRanges` object holds statistics for differentially methylated regions/bases.

### Author(s)

Pascal Belleau

### Examples

    ## Load permutation results on sites
    permutationResultsFile <- system.file("extdata",
        "permutationResultsForSites.RDS", package="methylInheritance")
    permutationResults <- readRDS(permutationResultsFile)

    ## Transform result to GRanges
    resultsGR <- methylInheritance:::getGRangesFromMethylDiff(methDiff =
        permutationResults, pDiff = 10, qvalue = 0.01, type = "hyper")

[Package methylInheritance version 1.18.0 Index]