GetSignInteractions {MACPET} | R Documentation

## Get the significant interactions of a `GenomeMap` object

### Description

`GetSignInteractions` subsets the significant interactions of a `GenomeMap` object given a user specified FDR cut-off. It returns/saves different kind of objects based on the `ReturnedAs` value.

### Usage

    GetSignInteractions(object, ...)

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

    ## S3 method for class 'GenomeMap'
    GetSignInteractions(object, threshold = NULL,
      ReturnedAs = "GInteractions", SaveTo = "", Prefix = "MACPET", ...)

    ## S4 method for signature 'GenomeMap'
    GetSignInteractions(object, threshold = NULL,
      ReturnedAs = "GInteractions", SaveTo = "", Prefix = "MACPET", ...)

### Arguments

`object` | An object of class `GenomeMap`.
`...` | Further arguments to be passed to `GetSignInteractions` (not used).
`threshold` | A numeric with the FDR cut-off threshold used to take a subset of significant interactions If `threshold=NULL` then all the interactions are returned.
`ReturnedAs` | What type of object to return. Possible values are: `'GInteractions'` Will return a `GInteractions` object. Each line corresponds to an interaction between two anchors (peaks). It provides information about the intervals of the peaks, the anchor/peak summits, the interaction p-value/FDR and order (see `GenomeMap` for further details). `'csv'` Will save a .csv file in the `SaveTo`. The file will be named after the `Prefix` parameter `Prefix_InteractionResults.csv`
`SaveTo` | The directory to save the csv file in case of `ReturnedAs=='csv'`.
`Prefix` | A string which will be used a prefix on the object saved in `SaveTo`.

### Details

`MACPETUlt` at Stage 4 will run the interaction analysis for the ChIA-PET data. This stage will proccess all the interactions in the data. After Stage 4 is run, the user can use the `GetSignInteractions` function on the saved object of class `GenomeMap`, to subset the significant interactions given a FDR cut-off.

### Value

For `GenomeMap` class, different outputs based on the `ReturnedAs` parameter.

### Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

### References

Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.

### See Also

`GenomeMap`

### Examples

    #load Interaction data: (class=GenomeMap)
    load(system.file('extdata', 'MACPET_GenomeMapData.rda', package = 'MACPET'))
    class(MACPET_GenomeMapData)
    GetSignInteractions(object=MACPET_GenomeMapData,
                        threshold = NULL,
                        ReturnedAs='GInteractions')

[Package MACPET version 1.6.0 Index]