TagsToGInteractions {MACPET} | R Documentation

## Convert PETs to GInteractions object

### 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, ioannis.vardaxis@ntnu.no

### References

Vardaxis I, Drabløs 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

[Package MACPET version 1.10.0 Index]