intersectPeakMatrix: intersectPeakMatrix

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

intersectPeakMatrix

Description

This function allows you to obtain the pair-wise intersected regions, along with the DNA methylation profiles, between two lists of peak sets, as well as (Meth)Motif logos

Usage

intersectPeakMatrix(
  peak_id_x,
  motif_only_for_id_x = FALSE,
  user_peak_list_x,
  user_peak_x_id,
  peak_id_y,
  motif_only_for_id_y = FALSE,
  user_peak_list_y,
  user_peak_y_id,
  methylation_profile_in_narrow_region = FALSE,
  external_source,
  motif_type = "MEME",
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

peak_id_x	Character of vector, each of which is a unique TFregulomeR ID.
motif_only_for_id_x	Either TRUE of FALSE (default). If TRUE, only peaks with motif will be loaded for each TFregulomeR ID in peak_id_x.
user_peak_list_x	A list of data.frames, each of which contains user's own bed-format peak regions for peak list x.
user_peak_x_id	Character of vector, each of which is a unique ID corresponding to each peak set in the list user_peak_list_x. 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.
peak_id_y	Character of vector, each of which is a unique TFregulomeR ID.
motif_only_for_id_y	Either TRUE of FALSE (default). If TRUE, only peaks with motif will be loaded for each TFregulomeR ID in peak_id_y.
user_peak_list_y	A list of data.frames, each of which contains user's own bed-format peak regions for peak list y.
user_peak_y_id	Character of vector, each of which is a unique ID corresponding to each peak set in the list user_peak_list_y. 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 intersected peak pair from peak_id_x (peak_id_y) and user_peak_list_x (user_peak_list_y) with TFregulomeR ID.
external_source	a bed-like data.frame files with the fourth column as the score to be profiled in pairwise comparison regions.
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 IntersectPeakMatrix class objects

Examples

peak_id_x <- c("MM1_HSA_K562_CEBPB", "MM1_HSA_HCT116_CEBPB")
peak_id_y <- c("MM1_HSA_HepG2_CEBPB", "MM1_HSA_HCT116_CEBPB")
intersectPeakMatrix_output <- intersectPeakMatrix(peak_id_x=peak_id_x,
                                                  motif_only_for_id_x=TRUE,
                                                  peak_id_y=peak_id_y,
                                                  motif_only_for_id_y=TRUE)

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