getGRangesFromMethylDiff: Transform results from a CpG site or region analysis done on...

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

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")

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