TagsToGInteractions {MACPET} | R Documentation |
TagsToGInteractions
converts the PETs of an object of PSFit
class to GInteractions
object.
TagsToGInteractions(object, ...) ## Default S3 method: TagsToGInteractions(object, ...) ## S3 method for class 'PSFit' TagsToGInteractions(object, threshold = NULL, ...)
object |
An object of class |
... |
(not used). |
threshold |
A numeric for the FDR threshold used to take a subset of
significant peaks/binding sites. If |
For PSFit
class:
A GInteractions
object containing PETs from all
the peaks found in the data (removing noisy and insignificant PETs).
Furthermore, it also includes information about
the binding sites which can be accessed via the
metadata
function.
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) object=TagsToGInteractions(object=MACPET_psfitData,threshold=1e-5) object S4Vectors::metadata(object)$Peaks.Info #peak/binding site information