exportPeaks: Exports peaks to csv file
In IoannisVardaxis/MACPET: Model based analysis for paired-end data

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

exportPeaks is an S3 method for the PSFit class. It exports peak information to a csv file in a given directory.

exportPeaks(object, ...)

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

## S3 method for class 'PSFit'
exportPeaks(object, file.out, savedir, threshold = NULL,
  ...)

## S4 method for signature 'PSFit'
exportPeaks(object, file.out, savedir,
  threshold = NULL, ...)

`object`	An object of `PSFit` class.
`...`	(not used).
`file.out`	A string with the name of the output to be saved to `savedir`.
`savedir`	A string with the directory to save the output.
`threshold`	A numeric indicating the FDR cut-off used for subseting significant peaks. If NULL all the peaks are returned.

For PSFit class: a csv file named after the value of file.out with all the information about the peaks found by the MACPETUlt function, plus comments which explain the column names.

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

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

PSFit

#Create a temporary forder, or anywhere you want:
savedir=file.path(tempdir(),'MACPETtest')
dir.create(savedir)#where you will save the results

#load Self-ligated data: (class=PSFit)
load(system.file('extdata', 'MACPET_psfitData.rda', package = 'MACPET'))
class(MACPET_psfitData)
exportPeaks(object=MACPET_psfitData,file.out='Peaks',threshold=1e-5,savedir=savedir)

#-----delete test directory:
unlink(savedir,recursive=TRUE)