Skip to contents

Minimally save a peak object to a file (BED4)

Source: R/save_peak_file.R
save_peak_file.Rd

This function saves a peak object to a file in BED4 format. The included columns are: chr, start, end, and name. Since no strand data is being included, it is recommended to use this function only for peak objects that do not have strand information.

Usage

save_peak_file(
  peak_obj,
  save = TRUE,
  filename = random_string(10),
  out_dir = tempdir()
)

Arguments

peak_obj

A GRanges object with the peak coordinates. Must include columns: seqnames, start, end, and name.

save

A logical indicating whether to save the peak object to a file.

filename

A character string of the file name. If the file extension is not .bed, a warning is issued and the extension is appended. Alternatively, if the file name does not have an extension, .bed is appended. (default = random string)

out_dir

A character string of the output directory. (default = tempdir())

Value

If save = FALSE, a data frame with the peak coordinates. If save = TRUE, the path to the saved file.

Examples

data("CTCF_ChIP_peaks", package = "MotifPeeker")

out <- save_peak_file(CTCF_ChIP_peaks, save = TRUE, "test_peak_file.bed")
print(out)
#> [1] "/tmp/RtmpIsNB8F/test_peak_file.bed"