exclusivePeakResult: exclusivePeaks result

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

exclusivePeaks result

Description

This function allows you to get the reuslts from the exclusivePeaks() output, including a list of exclusive peak sets, (Meth)Motif logo, methylation profile in exclsive peaks and exclsive peak summary.

Usage

exclusivePeakResult(
  exclusivePeaks,
  return_exclusive_peak_sites = FALSE,
  save_MethMotif_logo = FALSE,
  return_methylation_profile = FALSE,
  return_summary = FALSE,
  logo_type = "entropy",
  meth_level = "all"
)

Arguments

exclusivePeaks	Required. exclusivePeaks() output, a matrix of ExclusivePeaksMM class objects.
return_exclusive_peak_sites	Either TRUE of FALSE (default). If TRUE, a list of data.frames containing exclusive peak sets will be returned.
save_MethMotif_logo	Either TRUE of FALSE (default). If TRUE, (Meth)Motif logos for the exclusive peak sets will be saved.
return_methylation_profile	Either TRUE of FALSE (default). If TRUE, the methylation profiles in 200bp window around exclusive peak summits will be returned.
return_summary	Either TRUE of FALSE (default). If TRUE, a numeric matrix containing the percentage of peaks as exclusive will be returned.
logo_type	Logo type for the (Meth)Motif logo to be saved, either "entropy" (default) or "frequency".
meth_level	Methylation level to be plotted for the (Meth)Motif logo, and it should be one of the values, "all" (default), "methylated", and "unmethylated".

Value

a list of data.frames, a numeric matrix or (Meth)Motif logo PDF files depending on the options.

Examples

target_id <- "MM1_HSA_K562_CEBPB"
excluded_id <- c("MM1_HSA_HepG2_CEBPB", "MM1_HSA_HCT116_CEBPB")
excluPeak_output <- exclusivePeaks(target_peak_id=target_id,
                                   motif_only_for_target_peak=TRUE,
                                   excluded_peak_id=excluded_id,
                                   motif_only_for_excluded_peak=TRUE,
                                   methylation_profile_in_narrow_region=TRUE)
exclusivePeaks_result <- exclusivePeakResult(exclusivePeaks=excluPeak_output,
                                             return_exclusive_peak_sites=TRUE,
                                             save_MethMotif_logo=TRUE,
                                             return_summary=TRUE)

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