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

call_peaks_seacr

R Documentation

Call peaks: SEACR

Description

Call peaks from a bedGraph or bigWig file using SEACR (Sparse Enrichment Analysis for CUT&RUN).

Usage

call_peaks_seacr(
  bedgraph_path,
  control = 0.05,
  norm = TRUE,
  stringent = TRUE,
  outdir = tempdir(),
  outputfile = basename(tempfile(pattern = bedgraph_path, fileext = ".SEACR_peaks")),
  return_path = FALSE,
  remove_tmps = TRUE,
  nThread = 1,
  verbose = TRUE
)

Arguments

`bedgraph_path`	Field 1: Target data bedgraph file in UCSC bedgraph format that omits regions containing 0 signal.
`control`	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`).
`norm`	Field 3: "norm" (default: `norm=TRUE`) denotes normalization of control to target data, "non" (`norm=FALSE`) skips this behavior. "norm" is recommended unless experimental and control data are already rigorously normalized to each other (e.g. via spike-in).
`stringent`	Field 4:"relaxed" (`stringent=FALSE`) uses a total signal threshold between the knee and peak of the total signal curve, and corresponds to the “relaxed” mode described in the text, whereas “stringent” (default: `stringent=TRUE`) uses the peak of the curve, and corresponds to “stringent” mode.
`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.
`remove_tmps`	Remove temporary intermediate files generated by SEACR (i.e. )
`nThread`	When `nThread>1`, accelerates file importing and peak calling using multi-core parallelisation.
`verbose`	Print messages.