runMEME {TFBSTools} | R Documentation |
This function builds position frequency matrices using an external program MEME written by Bailey and Elkan.
## S4 method for signature 'character' runMEME(x, binary="meme", seqtype="DNA", arguments=list(), tmpdir=tempdir()) ## S4 method for signature 'DNAStringSet' runMEME(x, binary="meme", seqtype="DNA", arguments=list(), tmpdir=tempdir())
x |
A |
binary |
|
seqtype |
The sequence type. "AA" and "DNA" are allowed. |
arguments |
A |
tmpdir |
A |
A MotifSet
object is returned.
This wrapper is tested on “MEME” 4.10.1 and 4.12.0.
Ge Tan
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., et al. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic acids research, 37(Web Server issue), W202-8. doi:10.1093/nar/gkp335
## Not run: motifSet <- runMEME(file.path(system.file("extdata", package="TFBSTools"), "crp0.s"), binary="/usr/local/Cellar/meme/4.10.1/bin/meme", arguments=list("-nmotifs"=3)) ## Get the site sequences sitesSeq(motifSet, type="all") sitesSeq(motifSet, type="none") ## Get the consensu matrix, then it can be used as a PFMatrix consensusMatrix(motifSet) ## End(Not run)