interactome3D: interactome3D

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

interactome3D

Description

This function allows you to get a html report of a 3D dynamic TF interactome with CpG methylation and external source signal.

Usage

interactome3D(
  intersectPeakMatrix,
  return_interactome_with_mCpG = FALSE,
  mCpG_threshold = 0.8,
  return_interactome_with_external_source = FALSE,
  external_source_value = "median",
  angle_of_matrix = "x"
)

Arguments

intersectPeakMatrix	Output of function 'intersectPeakMatrix()'.
return_interactome_with_mCpG	Either TRUE of FALSE (default). If TRUE, html report of TF interactome with mCpG portion will be saved.
mCpG_threshold	A mininum beta score to determine CpG methylation. Should be 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 (default), or 0.9
return_interactome_with_external_source	Either TRUE of FALSE (default). If TRUE, html report of TF interactome with external source signal will be saved.
external_source_value	The value of external source signal in the intersected peaks. It should be one of the following values: "median" (default),"mean","SD","quartile_25","quartile_75".
angle_of_matrix	Either "x" (default) or "y". If "x", will focus on the peak sets in "peak_list_x" intersected with "peak_list_y"; if "y", will focus on peak sets in "peak_list_y" intersected with "peak_list_x".

Value

An html file

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