callPeaks,DsATAC-method | R Documentation |
Performs peak calling based on insertion sites
## S4 method for signature '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)
)
.object |
|
samples |
sample identifiers for which peak calling is performed |
method |
peak calling method. Currently only |
methodOpts |
list of other options depending on the |
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
GRangesList
of peak coordinates for each sample
Fabian Mueller
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