Peak calling with MACS2 — callPeak • pipelineNGS

Calls the peaks present in your sample bam files and returns bed files with the location of the enriched regions.

Usage

callPeak(
  file,
  path_peaks,
  path_logs,
  type_peak = "narrow",
  shift = FALSE,
  type = "SE"
)

file: Character string with the filename for the BAM file.
path_peaks: Character indicating the output directory for the peak files.
path_logs: Character indicating the output directory for the logs.
type_peak: Character indicating the type of peak to be called with MACS2, either "narrow" or "broad".
shift: Logical indicating whether the reads should be shifted -100bp and extended to 200bp (TRUE) or not (FALSE, default).
type: Sequence type, one of "SE" (single end) or "PE" (paired end).

Bed files in path_peaks with the location of the enriched regions.

if (FALSE) {
callPeak()
}