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

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

View source: R/dpeakMotif.R

Description

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

Usage

1
2
3
4
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

1
2
3
4
5
## Not run: 
library(BSgenome.Ecoli.NCBI.20080805)
resultMotif <- dpeakMotif( peakfile="examplePeak.txt", refGenome=Ecoli )

## End(Not run)

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