GetSignInteractions: Get the significant interactions of a 'GenomeMap' object

In IoannisVardaxis/MACPET: Model based analysis for paired-end data

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, [e-mail]

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')

IoannisVardaxis/MACPET documentation built on Aug. 9, 2019, 12:11 p.m.