intersectPeakMatrixResult: intersectPeakMatrix result

View source: R/intersectPeakMatrixResult.R

intersectPeakMatrixResultR Documentation

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.

Either TRUE of FALSE (default). If TRUE, (Meth)Motif logos for the intersected peaks will be saved.

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.