motifDistrib: profile TFBS distribution

In benoukraflab/TFregulomeR: TFregulomeR reveals transcription factors’ context-specific features and functions

profile TFBS distribution

Description

This function allows you to profile TFBS distributions in a given list of peak sets.

Usage

motifDistrib(
  id,
  peak_list,
  peak_id,
  plot_at_each_side = 100,
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

id	Required. TFregulomeR ID. The TFBS of interest to be profiled.
peak_list	Required. List of data.frames, each of which contains bed-format peak regions. They are the peak sets in which you want to profile the TFBS distributions, and can be loaded from TFregulomeR database or self-provided.
peak_id	Required. Character of vector, each of which is a unique ID corresponding to the element in "peak_list". If a peak set is orignally from TFregulomeR Database, its TFregulomeR ID should be used here.
plot_at_each_side	By default 100bp, and motif occurrences in a window of +/- 100bp around peak centres will be returned.
server	server localtion to be linked, either 'sg' or 'ca'.
TFregulome_url	TFregulomeR server is implemented in MethMotif server. If the MethMotif url is NO more "https://bioinfo-csi.nus.edu.sg/methmotif/" or "https://methmotif.org", please use a new url.
local_db_path	The complete path to the SQLite implementation of TFregulomeR database available at "https://methmotif.org/API_ZIPPED.zip"

Value

a list containing the numbers of input peaks and peaks with motif, as well as motif occurrences in the plot window.

Examples

CEBPB_peaks <- loadPeaks(id = "MM1_HSA_K562_CEBPB")
motifDistrib_output <- motifDistrib(id = "MM1_HSA_K562_CEBPB",
                                    peak_list = list(CEBPB_peaks[1:100,]),
                                    peak_id = "MM1_HSA_K562_CEBPB")

benoukraflab/TFregulomeR documentation built on July 8, 2024, 5:03 p.m.