Update the creb_peaks data.

neurogenomics · Apr 16, 2024 · 745e055 · 745e055
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diff --git a/R/creb_peaks.R b/R/creb_peaks.R
@@ -1,7 +1,17 @@
 #' CREB Peaks
 #'
 #' This dataset contains a set of CREB1 TIP-seq peaks (narrowPeak) produced by
-#' MACS3.
+#' MACS3 (first-mate, 5' shift). We have subset the peaks to reduce the data
+#' size (only chr19). The commands used to subset the data were:
+#'
+#' creb_peaks <- read.table("path/to/creb_peaks")
+#' creb_peaks <- creb_peaks[creb_peaks$V1 == "chr19",]
+#' write.table(creb_peaks,
+#'             "creb_subset.narrowPeak",
+#'             row.names = FALSE,
+#'             col.names = FALSE,
+#'             quote = FALSE,
+#'             sep = "\t")
 #'
 #' @format A GRanges peak object outputted by the \code{read_peak_file}
 #' function.

diff --git a/data-raw/creb_peaks.R b/data-raw/creb_peaks.R
@@ -1,2 +1,2 @@
-creb_peaks <- read_peak_file("inst/extdata/rep1_peaks.narrowPeak")
+creb_peaks <- read_peak_file("inst/extdata/creb_subset.narrowPeak")
 usethis::use_data(creb_peaks, overwrite = TRUE)
diff --git a/data/creb_peaks.rda b/data/creb_peaks.rda
diff --git a/inst/extdata/rep1_peaks.narrowPeak b/inst/extdata/rep1_peaks.narrowPeak
diff --git a/man/creb_peaks.Rd b/man/creb_peaks.Rd