qtlTFBSMotifEnrichment {MAGAR} | R Documentation

## 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)

[Package MAGAR version 1.2.0 Index]