create_triplet_regulon_based {MethReg} | R Documentation

## Map TF and target genes using regulon databases or any user provided target-tf. Maps TF to the DNAm region with TFBS using JASPAR2020 TFBS.

### Description

This function wraps two other functions `get_region_target_gene` and `get_tf_in_region` from the package.

### Usage

    create_triplet_regulon_based(
      region,
      genome = c("hg38", "hg19"),
      regulons.min.confidence = "B",
      motif.search.window.size = 0,
      motif.search.p.cutoff = 1e-08,
      cores = 1,
      tf.target,
      TF.peaks.gr = NULL,
      max.distance.region.target = 10^6
    )

### Arguments

`region` | A Granges or a named vector with regions (i.e "chr21:100002-1004000")
`genome` | Human genome reference "hg38" or "hg19"
`regulons.min.confidence` | Minimun confidence score ("A", "B","C","D", "E") classifying regulons based on their quality from Human DoRothEA database dorothea_hs. The default minimun confidence score is "B".
`motif.search.window.size` | Integer value to extend the regions. For example, a value of 50 will extend 25 bp upstream and 25 downstream the region. Default is no increase
`motif.search.p.cutoff` | motifmatchr pvalue cut-off. Default 1e-8.
`cores` | Number of CPU cores to be used. Default 1.
`tf.target` | A dataframe with tf and target columns. If not provided, dorothea_hs will be used.
`TF.peaks.gr` | A granges with TF peaks to be overlaped with input region Metadata column expected "id" with TF name. Default NULL. Note that Remap catalog can be used as shown in the examples.
`max.distance.region.target` | Max distance between region and target gene. Default 1Mbp.

### Value

A data frame with TF, target and RegionID information.

### Examples

    triplet <- create_triplet_regulon_based(
       region = c("chr1:69591-69592", "chr1:898803-898804"),
       motif.search.window.size = 50,
       regulons.min.confidence = "B",
         motif.search.p.cutoff = 0.05
    )

[Package MethReg version 1.4.0 Index]