runMEME {TFBSTools} | R Documentation

## Wrapper function for MEME

### 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)

[Package TFBSTools version 1.26.0 Index]