create_triplet_regulon_based: Map TF and target genes using regulon databases or any user...

In TransBioInfoLab/MethReg: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

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
)

TransBioInfoLab/MethReg documentation built on July 28, 2023, 9:17 p.m.