commonPeaks: commonPeaks

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

commonPeaks

Description

This function allows you to obtain a list of common peak subsets along with the DNA methylation profiles.

Usage

commonPeaks(
  target_peak_id,
  motif_only_for_target_peak = FALSE,
  user_target_peak_list,
  user_target_peak_id,
  compared_peak_id,
  motif_only_for_compared_peak = FALSE,
  user_compared_peak_list,
  user_compared_peak_id,
  methylation_profile_in_narrow_region = TRUE,
  motif_type = "MEME",
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

target_peak_id	Character of vector, each of which is a TFregulomeR ID. Each of target peak will be compared with all "compared peaks" to get its common subset.
motif_only_for_target_peak	Either TRUE of FALSE (default). If TRUE, only peaks with motif will be loaded for each TFregulomeR ID in target_peak_id.
user_target_peak_list	A list of data.frames, each of which contains user's own bed-format target peak regions.
user_target_peak_id	Character of vector, each of which is a unique ID corresponding to each peak set in the list user_target_peak_list. If the IDs are not provided or not unique, the function will automatically generate the IDs of its own. If any of the peak sets is derived from TFregulomeR, its TFregulomeR ID should be used here correspondingly.
compared_peak_id	Character of vector, each of which is a TFregulomeR ID.
motif_only_for_compared_peak	Either TRUE of FALSE (default). If TRUE, only peaks with motif will be loaded for each TFregulomeR ID in compared_peak_id.
user_compared_peak_list	A list of data.frames, each of which contains user's own bed-format compared peak regions.
user_compared_peak_id	Character of vector, each of which is a unique ID corresponding to each peak set in the list user_compared_peak_list. If the IDs are not provided or not unique, the function will automatically generate the IDs of its own. If any of the peak sets is derived from TFregulomeR, its TFregulomeR ID should be used here correspondingly.
methylation_profile_in_narrow_region	Either TRUE (default) of FALSE. If TRUE, methylation states in 200bp window surrounding peak summits for each common peak from target_peak_id and user_target_peak_list with TFregulomeR ID.
motif_type	Motif PFM format, either in MEME by default or TRANSFAC.
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

matrix of CommonPeaksMM class objects

Examples

target_id <- c("MM1_HSA_K562_CEBPB")
compared_id <- c("MM1_HSA_HepG2_CEBPB")
commonPeaks_output <- commonPeaks(target_peak_id=target_id,
                                  motif_only_for_target_peak=TRUE,
                                  compared_peak_id=compared_id,
                                  motif_only_for_compared_peak=TRUE,
                                  methylation_profile_in_narrow_region=TRUE)

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