dpeakMotif: Implement de novo motif analysis based on the peak list

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

Description

Implement de novo motif analysis based on the peak list, using MEME and FIMO.

Usage

dpeakMotif( peakfile=NULL, refGenome=NULL, flanking=100,
	memeArgument="-dna -mod zoops -nmotifs 1 -minw 10 -maxw 20 -revcomp -maxsize 1000000000", 
	fimoArgument="-max-stored-scores 100000000 -motif-pseudo 0.000001",
    tempDir=NULL )

Arguments

peakfile	File name of the peak list.
refGenome	BSgenome class object to extract sequences.
flanking	Flanking length.
memeArgument	Parameters for MEME.
fimoArgument	Parameters for FIMO.
tempDir	Directory of temporary files for sequence extraction, MEME, and FIMO.

Details

The first three columns of the peak list file (specifed as peakfile) are assumed to be chromosome, start and end positions of each peak region. There should be no header in the peak list file.

refGenome is a BSgenome class object and assumed to already be available in the R environment.

Value

Construct DpeakMotif class object.

Author(s)

Dongjun Chung

See Also

dpeakFit, DpeakMotif.

Examples

## Not run: 
library(BSgenome.Ecoli.NCBI.20080805)
resultMotif <- dpeakMotif( peakfile="examplePeak.txt", refGenome=Ecoli )
resultMotif
fitPET <- dpeakFit( dataPET, resultMotif )

## End(Not run)

dongjunchung/dpeak documentation built on March 1, 2020, 3:44 a.m.