callPeaks-methods — callPeaks,DsATAC-method • ChrAccR

Performs peak calling based on insertion sites

# S4 method for DsATAC
callPeaks(
  .object,
  samples = getSamples(.object),
  method = "macs2_summit_fw_no",
  methodOpts = list(macs2.exec = "macs2", macs2.params = c("--shift", "-75",
    "--extsize", "150", "-p", "0.01"), fixedWidth = 250, genomeSizesFromObject = FALSE)
)

Arguments

.object: DsATAC object
samples: sample identifiers for which peak calling is performed
method: peak calling method. Currently only 'macs2_summit_fw_no' is supported. See details section.
methodOpts: list of other options depending on the 'method' parameter (see details section).

Value

GRangesList of peak coordinates for each sample

Details

The following methods are currently supported

'macs2_summit_fw_no': Fixed-width, non-overlapping peaks based on MACS2 summit calls: 1. Call peaks using system call to MACS2. You can specify the MACS2 executable in methodOpts$macs2.exec. 2. Identify peak summits 3. extend peak summits on each side by a number of basepairs (specified in methodOpts$fixedWidth; default: 250bp) to obtain unified peak widths 4. Find non-overlapping peaks by taking the peak with the best MACS2 score from each set of partially overlapping peaks

Author

Fabian Mueller