## ----setup_vignette----------------------------------------------------------- library(EpiCompare) ## ----------------------------------------------------------------------------- data("encode_H3K27ac") # ENCODE ChIP-seq data("CnT_H3K27ac") # CUT&Tag data("CnR_H3K27ac") # CUT&Run data("hg19_blacklist") # hg19 genome blacklist data("CnT_H3K27ac_picard") # CUT&Tag Picard summary output data("CnR_H3K27ac_picard") # CUT&Run Picard summary output ## ----------------------------------------------------------------------------- peaklist <- list(CnT_H3K27ac, CnR_H3K27ac) # create list of peakfiles names(peaklist) <- c("CnT", "CnR") # set names ## ----------------------------------------------------------------------------- # create list of Picard summary picard <- list(CnT_H3K27ac_picard, CnR_H3K27ac_picard) names(picard) <- c("CnT", "CnR") # set names ## ----------------------------------------------------------------------------- reference_peak <- list("ENCODE_H3K27ac" = encode_H3K27ac) ## ----------------------------------------------------------------------------- EpiCompare(peakfiles = peaklist, genome_build = "hg19", blacklist = hg19_blacklist, picard_files = picard, reference = reference_peak, upset_plot = FALSE, stat_plot = FALSE, chromHMM_plot = FALSE, chromHMM_annotation = "K562", chipseeker_plot = FALSE, enrichment_plot = FALSE, tss_plot = FALSE, interact = FALSE, save_output = FALSE, output_filename = "EpiCompare_test", output_timestamp = FALSE, output_dir = tempdir()) ## ----Session_Info_vignette---------------------------------------------------- utils::sessionInfo()