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) )
sample identifiers for which peak calling is performed
peak calling method. Currently only
'macs2_summit_fw_no' is supported. See details section.
list of other options depending on the
'method' parameter (see details section).
GRangesList of peak coordinates for each sample
The following methods are currently supported
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
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