motifDistrib: profile TFBS distribution

In linquynus/TFregulomeR-dev: 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 = "sg", TFregulome_url)

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 "http://bioinfo-csi.nus.edu.sg/methmotif/" or "http://methmotif.org", please use a new url.

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")

linquynus/TFregulomeR-dev documentation built on April 23, 2022, 11:11 a.m.