qtlBaseSubstitutionEnrichment: qtlBaseSubstitutionEnrichment

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

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)

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