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

Description Usage Arguments Value Examples

View source: R/create_triplet_regulon_based.R

Description

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

Usage

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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

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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
)

MethReg documentation built on Nov. 8, 2020, 8:01 p.m.