PeaksToGRanges {MACPET} | R Documentation |
PeaksToGRanges
converts peaks of an object of PSFit
class to GRanges
object.
PeaksToGRanges(object, ...) ## Default S3 method: PeaksToGRanges(object, ...) ## S3 method for class 'PSFit' PeaksToGRanges(object, threshold = NULL, ...) ## S4 method for signature 'PSFit' PeaksToGRanges(object, threshold = NULL, ...)
object |
An object of class |
... |
Further arguments to be passed to |
threshold |
A numeric with the FDR cut-off threshold used to take a
subset of significant peaks. If |
PeaksToGRanges
converts peak information into a
GRanges
object. Each row in the
GRanges
object represents a peak with 'CIQ.Up.start' and 'CIQ.Down.end' as start
and end coordinates, respectively (see PSFit
)
Metadata will also include information for the total PETs,
the p-value and the FDR of each peak.
For PSFit
class, a
GRanges
object created by the estimated
peak information including metadata columns for the total PETs,
the p-value and the FDR of each peak.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.
#load Self-ligated data: (class=PSFit) load(system.file('extdata', 'MACPET_psfitData.rda', package = 'MACPET')) class(MACPET_psfitData) PeaksToGRanges(object=MACPET_psfitData,threshold=1e-5)