loadPeaks: load peaks from TFregulomeR

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

load peaks from TFregulomeR

Description

This function allows you to obtain the peaks from TFregulomeR using TFregulomeR ID.

Usage

loadPeaks(
  id,
  includeMotifOnly = FALSE,
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

id	Required. TFregulomeR ID
includeMotifOnly	Either TRUE or FALSE (default). If TRUE, only peaks with motif 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_TFregulomeR/downloads/"

Value

a data.frame containing peak coordinates

Examples

CEBPB_peaks <- loadPeaks(id = "MM1_HSA_K562_CEBPB")

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