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")

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