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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/GetSignInteractions-methods.R

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

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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, Drabl<c3><b8>s F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.

See Also

GenomeMap

Examples

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#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')

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