qtlBaseSubstitutionEnrichment {MAGAR} | R Documentation

## qtlBaseSubstitutionEnrichment

### Description

This function tests for enrichment of a specific base substitution in the methQTL interactions.

### Usage

    qtlBaseSubstitutionEnrichment(meth.qtl.res, merge = FALSE)

### Arguments

`meth.qtl.res` | An object of type `MethQTLResult-class` or a list of such objects.
`merge` | Flag indicating if 5' and 3' substitutions are to be merged or to be analyzed separately.

### Details

The names of the list are e.g. `A_G`, which refers to a replacement of the reference base `A` with an `A`. Enrichment is computed using Fisher's exact test, using all SNP that have been used as input as the background.

### Value

A list with one element for each potential base substitution containing the enrichment p-value.

### Author(s)

Michael Scherer

### Examples

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

[Package MAGAR version 1.0.1 Index]