commonPeakResult: commonPeaks result

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

commonPeaks result

Description

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

Usage

commonPeakResult(
  commonPeaks,
  return_common_peak_sites = FALSE,
  save_MethMotif_logo = FALSE,
  return_methylation_profile = FALSE,
  return_summary = FALSE,
  logo_type = "entropy",
  meth_level = "all"
)

Arguments

commonPeaks	Required. commonPeaks() output, a matrix of CommonPeaksMM class objects.
return_common_peak_sites	Either TRUE of FALSE (default). If TRUE, a list of data.frames containing common peak sets.
save_MethMotif_logo	Either TRUE of FALSE (default). If TRUE, (Meth)Motif logos for the common peak sets will be saved.
return_methylation_profile	Either TRUE of FALSE (default). If TRUE, the methylation profiles in 200bp window around common peak summits will be returned.
return_summary	Either TRUE of FALSE (default). If TRUE, a numeric matrix containing the percentage of peaks as common 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 <- 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)
commonPeaks_result <- commonPeakResult(commonPeaks=commonPeaks_output,
                                       return_common_peak_sites=TRUE,
                                       save_MethMotif_logo=TRUE,
                                       return_methylation_profile=TRUE,
                                       return_summary=TRUE)

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