exportMMPFM: export motif position frequency matrix and beta score matrix

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

export motif position frequency matrix and beta score matrix

Description

This function allows you to export motif position frequency matrix and beta score matrix from the output of " searchMotif", "commonPeaks", "exclusivePeaks" or "intersectPeakMatrix".

Usage

exportMMPFM(
  fun_output,
  fun,
  save_motif_PFM = FALSE,
  save_betaScore_matrix = FALSE,
  angle_of_matrix_for_intersectPeakMatrix = "x",
  saving_id_x_for_intersectPeakMatrix = "all",
  saving_id_y_for_intersectPeakMatrix = "all"
)

Arguments

fun_output	Required. Output from "searchMotif", "commonPeaks", "exclusivePeaks" or "intersectPeakMatrix".
fun	Required. The function that was used to get the output and should be one of the options, 'searchMotif', 'commonPeaks', 'exclusivePeaks' and 'intersectPeakMatrix'.
save_motif_PFM	Either TRUE or FALSE (default). If "TRUE", the motif position frequency matrix will be saved.
save_betaScore_matrix	Either TRUE or FALSE (default). If "TRUE", the beta score matrix will be saved.
angle_of_matrix_for_intersectPeakMatrix	Only applicable when "fun='intersectPeakMatrix'". Either "x" (default) or "y". If "x", motif PFM for the peak sets in "peak_list_x" intersected with "peak_list_y" will be saved; if "y", motif PFM for the peak sets in "peak_list_y" intersected with "peak_list_x" will be saved.
saving_id_x_for_intersectPeakMatrix	Only applicable when "fun='intersectPeakMatrix'". Either "all" (default) or a subset of "peak_id_x". If a subset of "peak_id_x" is provided, only the MethMotif logos for them will be saved.
saving_id_y_for_intersectPeakMatrix	Only applicable when "fun='intersectPeakMatrix'". Either "all" (default) or a subset of "peak_id_y". If a subset of "peak_id_y" is provided, only the MethMotif logos for them will be saved.

Value

motif position frequency matrix file and beta score matrix file

Examples

methmotif_cebpb <- searchMotif(id = "MM1_HSA_K562_CEBPB")
exportMMPFM(fun_output = methmotif_cebpb, fun = "searchMotif",
            save_motif_PFM = TRUE, save_betaScore_matrix = TRUE)

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