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

pooled_peaks_seacr

R Documentation

Call consensus peaks: SEACR

Call consensus peaks by merging groups of BAM files with mergeBam and then calling peaks with call_peaks_seacr.

pooled_peaks_seacr(
  bam_files,
  outdir = tempdir(),
  g = NULL,
  overwrite = TRUE,
  nThread = 1,
  verbose = TRUE,
  ...
)

`bam_files`	One or more BAM files.
`outdir`	Directory to save results to.
`verbose`	Print messages.
`...`	Arguments passed on to `call_peaks_seacr` `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. `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. `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.