intersectPeakMatrixResult: intersectPeakMatrix result

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

intersectPeakMatrix result

Description

This function allows you to get the reuslts from the intersectPeakMatrix() output, including a matrix of the pair-wise intersecting percentages between two lists of peak sets, DNA methylation profiles in the intersected regions (for peaks from TFregulomeR) and (Meth)Motif logos for each pair of intersections (for peaks from TFregulomeR).

Usage

intersectPeakMatrixResult(
  intersectPeakMatrix,
  return_intersection_matrix = FALSE,
  angle_of_matrix = "x",
  return_tag_density = FALSE,
  angle_of_tag_density = "x",
  tag_density_value = "median",
  return_external_source = FALSE,
  angle_of_external_source = "x",
  external_source_value = "median",
  return_methylation_profile = FALSE,
  angle_of_methylation_profile = "x",
  save_MethMotif_logo = FALSE,
  angle_of_logo = "x",
  logo_type = "entropy",
  meth_level = "all",
  saving_MethMotif_logo_x_id = "all",
  saving_MethMotif_logo_y_id = "all"
)

Arguments

intersectPeakMatrix	Required. intersectPeakMatrix() output, a marix of IntersectPeakMatrix class objects.
return_intersection_matrix	Either TRUE of FALSE (default). If TRUE, a matrix of the pair-wise intersecting percentages between two lists of peak sets will be returned.
angle_of_matrix	Either "x" (default) or "y". If "x", a matrix denoting the percentages of peak sets in "peak_list_x" intersected with "peak_list_y" will be returned; if "y", a matrix denoting the percentages of peak sets in "peak_list_y" intersected with "peak_list_x" will be returned.
return_tag_density	Either TRUE of FALSE (default). If TRUE, a matrix of tag density values in intersected peaks between "peak_list_x" and "peak_list_y" will be returned.
angle_of_tag_density	Either "x" (default) or "y". If "x", a matrix denoting tag density values in "peak_list_x" intersected with "peak_list_y" will be returned; if "y", a matrix denoting tag density values in "peak_list_y" intersected with "peak_list_x" will be returned.
tag_density_value	The value of tag density in the intersected peaks. It should be one of the following values: "median" (default),"mean","SD","quartile_25","quartile_75".
return_external_source	Either TRUE of FALSE (default). If TRUE, a matrix of external source values in intersected peaks between "peak_list_x" and "peak_list_y" will be returned.
angle_of_external_source	Either "x" (default) or "y". If "x", a matrix denoting external source values in "peak_list_x" intersected with "peak_list_y" will be returned; if "y", a matrix denoting tag density values in "peak_list_y" intersected with "peak_list_x" will be returned.
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".
return_methylation_profile	Either TRUE of FALSE (default). If TRUE, a matrix of DNA methylation state data in the intersected regions will be returned.
angle_of_methylation_profile	Either "x" (default) or "y". If "x", a matrix denoting DNA methylation state data in "peak_list_x" intersected with "peak_list_y" will be returned; if "y", a matrix denoting DNA methylation state data in "peak_list_y" intersected with "peak_list_x" will be returned.
save_MethMotif_logo	Either TRUE of FALSE (default). If TRUE, (Meth)Motif logos for the intersected peaks will be saved.
angle_of_logo	Either "x" (default) or "y". If "x", (Meth)Motif logos for the peak sets in "peak_list_x" intersected with "peak_list_y" will be saved; if "y", (Meth)Motif logos for the peak sets in "peak_list_y" intersected with "peak_list_x" will be saved.
logo_type	Logo type for the (Meth)Motif logo to be saved, either "entropy" (default) or "frequency".
meth_level	Methylation level to be plot for the (Meth)Motif logo, and it should be one of the values, "all" (default), "methylated", and "unmethylated".
saving_MethMotif_logo_x_id	Either "all" (default) or a subset of "peak_id_x". If a subset of "peak_id_x" is provided, only the (Meth)Motif logos for them will be saved.
saving_MethMotif_logo_y_id	Either "all" (default) or a subset of "peak_id_y". If a subset of "peak_id_y" is provided, only the (Meth)Motif logos for them will be saved.

Value

a matrix of pair-wise intersecting percantages between two lists of peak sets, a matrix of DNA methylation data in the intersected regions or (Meth)Motif PDF files depending on the options

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")
intersect_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)
intersect_matrix <- intersectPeakMatrixResult(intersectPeakMatrix=intersect_output,
                                              return_intersection_matrix=TRUE,
                                              save_MethMotif_logo=TRUE,
                          saving_MethMotif_logo_x_id=c("MM1_HSA_K562_CEBPB"))

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