runMEME-methods: Wrapper function for MEME

In TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

Description

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

Usage

  ## 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())

Arguments

x	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.

Note

This wrapper is tested on “MEME” 4.10.1 and 4.12.0.

Author(s)

Ge Tan

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/

See Also

MotifSet

Examples

  ## 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)

TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.