runMEME: Wrapper function for MEME

Description

This function builds position frequency matrices using an external program MEME written by Bailey and Elkan.

Usage

"runMEME"(x, binary="meme", seqtype="DNA",  arguments=list(), tmpdir=tempdir()) "runMEME"(x, binary="meme", seqtype="DNA",  arguments=list(), tmpdir=tempdir())

Arguments

A character(1) vector of the path of fasta file or a XStringSet.

binary

character(1): the path of MEME binary. By default, we assume the meme is in the PATH.

seqtype

The sequence type. "AA" and "DNA" are allowed.

arguments

A list: the addtional arguments for meme. This list takes the parameter of MEME as names of the elements, and the values of the parameters as the elements. For examples, arguments=list("-nmotifs"=3).

tmpdir

A character(1) vector to change the defult R's temp directory.

Value

A MotifSet object is returned.

References

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 http://meme-suite.org/

Examples

Run this code

  ## 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)