PeaksToGRanges: Convert peaks to GRanges object

In MACPET: Model based analysis for paired-end data

Description

PeaksToGRanges converts peaks of an object of PSFit class to GRanges object.

Usage

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, ...)

Arguments

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.

Details

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.

Value

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.

Author(s)

Ioannis Vardaxis, [e-mail]

References

Vardaxis I, Drabl<c3><b8>s F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.

See Also

PSFit, PeaksToNarrowPeak

Examples

#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)

MACPET documentation built on Nov. 8, 2020, 5:47 p.m.