PeaksToGRanges: Convert peaks to GRanges object
In IoannisVardaxis/MACPET: Model based analysis for paired-end data

Description Usage Arguments Details Value Author(s) References See Also Examples

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 `PSFit`.
`...`	Further arguments to be passed to `PeaksToGRanges` (not used).
`threshold`	A numeric with the FDR cut-off threshold used to take a subset of significant peaks. If `threshold=NULL` then all the peaks are returned.

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.

PSFit, PeaksToNarrowPeak

#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)