exportPeakList: Export deconvolution results to text files

In carter-allen/dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

Description

Export deconvolution results to text files in TXT, BED, or GFF file formats.

Usage

exportPeakList(object, ...)
## S4 method for signature 'DpeakFit'
exportPeakList( object, type=NA, filename=NA, ... )

Arguments

object	Object of class DpeakFit, deconvolution model fits obtained using the method dpeakFit.
type	Format of the exported file. Possible values are "txt", "bed", and "gff". See Details.
filename	Name of the exported file.
...	Other parameters to be passed through to generic exportPeakList.

Details

Columns of TXT file format (type="txt") include chromosome, binding site, relative binding strength in each peak region, and the peak region that each binding event belongs to. type="bed" and type="gff" export deconvolution results in standard BED and GFF file formats, respectively, where score is the relative binding strength multiplied by 1000. The feature of GFF file and the name of BED file are the peak region that each binding event belongs to.

Value

Export deconvolution results to text files

Author(s)

Dongjun Chung

See Also

dpeakFit, DpeakFit.

Examples

data(exampleData)
fit <- dpeakFit(exampleData)
exportPeakList( fit, type="txt", filename="result.txt" )
exportPeakList( fit, type="bed", filename="result.bed" )
exportPeakList( fit, type="gff", filename="result.gff" )

carter-allen/dpeak documentation built on April 23, 2020, 4:09 p.m.