cofactorReport: cofactorReport

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

cofactorReport

Description

This function allows you to get a PDF report of top cofactors along with DNA methylation for a TF.

Usage

cofactorReport(intersectPeakMatrix, top_num = 10,
  cobinding_threshold = 0.05)

Arguments

intersectPeakMatrix	Output of function 'intersectPeakMatrix()'.
top_num	Number of highest co-binding factors to report for each TF (up to 10). By default the number is 10.
cobinding_threshold	Only the co-factors with co-binding percentages more than this threshold value will be reported. By default the threshold is 0.05.

Value

A PDF file

Examples

peak_id_x <- c("MM1_HSA_K562_CEBPB")
peak_id_y <- c("MM1_HSA_K562_CEBPD", "MM1_HSA_K562_ATF4")
intersect_output <- intersectPeakMatrix(peak_id_x=peak_id_x,
                                        motif_only_for_id_x=TRUE,
                                        peak_id_y=peak_id_y)
cofactorReport(intersectPeakMatrix = intersect_output)

linquynus/TFregulomeR-dev documentation built on April 23, 2022, 11:11 a.m.