## ----eval=TRUE, echo=TRUE----------------------------------------------------- # Load necessary libraries suppressPackageStartupMessages(library(BiFET)) suppressPackageStartupMessages(library(GenomicRanges)) library(BiFET) library(GenomicRanges) peak_file <- system.file("extdata", "input_peak_motif.Rdata", package = "BiFET") load(peak_file) # Display the first few rows and columns of the peak file head(GRpeaks) ## ----eval=TRUE, echo=TRUE----------------------------------------------------- # Display the first few rows and columns of the motif file head(GRmotif) ## ----eval=TRUE, echo=TRUE----------------------------------------------------- # call the function “calculate_enrich_p” to return a list of # parameter alpha_k, enrichment p values from BiFET algorithm # and enrichment p values from the hypergeometric test : result <- calculate_enrich_p(GRpeaks, GRmotif) head(result)