dpeakMotif {dpeak} | R Documentation |
Implement de novo motif analysis based on the peak list, using MEME and FIMO.
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 )
peakfile |
File name of the peak list. |
refGenome |
|
flanking |
Flanking length. |
memeArgument |
Parameters for |
fimoArgument |
Parameters for |
tempDir |
Directory of temporary files for sequence extraction, MEME, and FIMO. |
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.
Construct DpeakMotif
class object.
Dongjun Chung
## Not run: library(BSgenome.Ecoli.NCBI.20080805) resultMotif <- dpeakMotif( peakfile="examplePeak.txt", refGenome=Ecoli ) ## End(Not run)