qtlAnnotationEnrichment: qtlAnnotationEnrichment

In MPIIComputationalEpigenetics/MAGAR: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

qtlAnnotationEnrichment

Description

This functions performs enrichment analysis using the Fisher's test for the methQTLs detected with respect to different genomic annotations.

Usage

qtlAnnotationEnrichment(
  meth.qtl.res,
  type = "SNP",
  annotation = "cpgislands",
  assembly = "hg19"
)

Arguments

meth.qtl.res	An object of type MethQTLResult-class or a list of such objects.
type	The type of methQTL to be visualized. Can be either 'SNP', 'CpG', or 'cor.block'
annotation	The genomic annotation to be used. Can be the ones available in rnb.region.types or "ctcf", "distal", "dnase", "proximal", "tfbs", "tss"
assembly	The assembly used. Only "hg19" (default) and "hg38" supported.

Details

We use all data points that have been used to calculate methQTLs as the background and compare the overlaps with the annotation of interest in comparison to the methQTLs that have been computed in case a MethQTLResult-class is provided. If a list of MethQTLResult-class objects is provided, the intersection between the methQTLs from all objects in the list is compared with the union of all interactions that have been tested.

Value

A list of two p-values named 'enrichment' for overrepresentation and 'depletion' for underrepresentation

Author(s)

Michael Scherer

Examples

meth.qtl.res <- loadMethQTLResult(system.file("extdata","MethQTLResult_chr18",package="MAGAR"))
res <- qtlAnnotationEnrichment(meth.qtl.res)

MPIIComputationalEpigenetics/MAGAR documentation built on Dec. 6, 2024, 2:30 p.m.