## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- library(MACSr) ## ----------------------------------------------------------------------------- eh <- ExperimentHub::ExperimentHub() eh <- AnnotationHub::query(eh, "MACSdata") CHIP <- eh[["EH4558"]] CTRL <- eh[["EH4563"]] ## ----------------------------------------------------------------------------- cp1 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE, name = "run_callpeak_narrow0", outdir = tempdir(), cutoff_analysis = TRUE) cp2 <- callpeak(CHIP, CTRL, gsize = 5.2e7, store_bdg = TRUE, name = "run_callpeak_broad", outdir = tempdir(), broad = TRUE) ## ----------------------------------------------------------------------------- cp1 cp2 ## ----------------------------------------------------------------------------- cp1$arguments ## ----------------------------------------------------------------------------- cp1$outputs ## ----------------------------------------------------------------------------- cat(cp1$log) ## ----------------------------------------------------------------------------- sessionInfo()