qtlAnnotationEnrichment {MAGAR} | R Documentation

## 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")

### 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"`

### 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)

[Package MAGAR version 1.2.0 Index]