TagsToGInteractions: Convert PETs to GInteractions object

In MACPET: Model based analysis for paired-end data

Description

TagsToGInteractions converts the PETs of an object of PSFit class to GInteractions object.

Usage

TagsToGInteractions(object, ...)

## Default S3 method:
TagsToGInteractions(object, ...)

## S3 method for class 'PSFit'
TagsToGInteractions(object, threshold = NULL, ...)

## S4 method for signature 'PSFit'
TagsToGInteractions(object, threshold = NULL, ...)

Arguments

object	An object of class PSFit.
...	(not used).
threshold	A numeric for the FDR threshold used to take a subset of significant peaks/binding sites. If threshold=NULL then all the peaks are returned.

Value

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.

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

Examples

#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

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