| exportPeaks {MACPET} | R Documentation |
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 |
... |
(not used). |
file.out |
A string with the name of the output to be saved to
|
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.
#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)