GetSignInteractions {MACPET} | R Documentation |
GenomeMap
objectGetSignInteractions
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.
GetSignInteractions(object, ...) ## Default S3 method: GetSignInteractions(object, ...) ## S3 method for class 'GenomeMap' GetSignInteractions(object, threshold = NULL, ReturnedAs = "GInteractions", SaveTo = "", Prefix = "MACPET", ...)
object |
An object of class |
... |
Further arguments to be passed to |
threshold |
A numeric with the FDR cut-off threshold used to take a
subset of significant interactions If |
ReturnedAs |
What type of object to return. Possible values are:
|
SaveTo |
The directory to save the csv file in case of |
Prefix |
A string which will be used a prefix on the object saved in |
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.
For GenomeMap
class, different outputs based on the ReturnedAs
parameter.
Ioannis Vardaxis, ioannis.vardaxis@ntnu.no
Vardaxis I, Drabløs F, Rye M and Lindqvist BH (2018). MACPET: Complete pipeline for ChIA-PET. To be published.
#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')