callPeak: Peak calling with MACS2

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Peak calling with MACS2

Description

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"
)

Arguments

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).

Value

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

Examples

## Not run: 
callPeak()

## End(Not run)

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.