call_peaks_macsr: Call peaks: MACSr
In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

call_peaks_macsr

R Documentation

Call peaks: MACSr

Description

Call peaks from a bedGraph or bigWig file using MACS3/MACSr. By default, it automatically infers a reasonable cutoff threshold as well.
Note : MACS3/MACSr is not currently compatible with Windows (see here for details).

Usage

call_peaks_macsr(
  bedgraph_path,
  cutoff = NULL,
  minlen = 200L,
  maxgap = 30L,
  call_summits = TRUE,
  trackline = TRUE,
  log = TRUE,
  outdir = tempdir(),
  outputfile = "MACSr.peaks.bed",
  return_path = FALSE,
  verbose = TRUE
)

Arguments

`bedgraph_path`	Path to bedGraph file. Can instead provide a bigWig file, but this will first be converted to bedGraph format, which can take some time if trying to convert data from across the entire genome.
`cutoff`	when `method="MACSr"` : Passed to `cutoff` argument. Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS3, score 5 means pvalue 1e-5. If `NULL`, a reasonable `cutoff` value will be inferred through a `cutoff_analysis`. when `method="SEACR"` : Passed to `control` argument. Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. Alternatively, a numeric threshold n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks (default: `0.05`).
`minlen`	minimum length of peak, better to set it as d value. DEFAULT: 200", default = 200.
`maxgap`	maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30", default = 30.
`call_summits`	If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region DEFAULT: False",default=False.
`trackline`	Tells MACS not to include trackline with bedGraph files. The trackline is used by UCSC for the options for display.
`log`	Whether to capture logs.
`outdir`	Directory to store `cutoff_analysis` report and peak file in.
`outputfile`	Name of the peak output file (stored in BED format).
`return_path`	Whether to return the path to the saved peak file, or the peak data itself as a GRanges object.
`verbose`	Print messages.