qtlTFBSMotifEnrichment: qtlTFBSMotifEnrichment

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

qtlTFBSMotifEnrichment

Description

This function performs TFBS enrichment analysis for the methQTL SNPs/CpGs detected and returns overrepresented binding motifs.

Usage

qtlTFBSMotifEnrichment(
  meth.qtl.res,
  type = "SNP",
  size = 500,
  assembly = "hg19",
  subsample = 1e+05,
  out.dir = getwd(),
  ...
)

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'
size	Motif enrichment is only supported for genomic regions. Therefore, we resize the invididual methQTL to genomic regions using a width of this size around the site of interest.
assembly	The assembly used. Only "hg19" and "hg38" supported
subsample	Integer specifying how many of the regions are to be subsamples from the universe.
out.dir	The output directory in which resulting plots will be stored.
...	Further parameters passed to findMotifFgBg

Details

This function is in part based on the tutorial for Motif discovery in https://compgenomr.github.io/book/motif-discovery.html. 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 plot describing the TFB motif enrichment

Author(s)

Michael Scherer

Examples

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

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