dpeakMotif {dpeak} | R Documentation

## Implement de novo motif analysis based on the peak list

### 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 )

    ## End(Not run)

[Package dpeak version 1.6.0 Index]