exportPeaks: Exports peaks to csv file

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

View source: R/exportPeaks-methods.R

Description

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

Usage

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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, ...)

Arguments

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.

Value

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.

Author(s)

Ioannis Vardaxis, ioannis.vardaxis@ntnu.no

References

Vardaxis I, Drabl<c3><b8>s F, Rye M and Lindqvist BH (2018). MACPET: Model-based Analysis for ChIA-PET. To be published.

See Also

PSFit

Examples

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#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)

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