run_meme {universalmotif} | R Documentation

## Run MEME from within R.

### Description

De novo motif discovery via MEME. For a detailed description of the command, see http://meme-suite.org/doc/meme.html. For a brief description of the command parameters, call `run_meme()` without any arguments. Parameters in `run_meme()` which are directly taken from the MEME program are tagged with [MEME]. This function requires that the processx package be installed separately.

### Usage

    run_meme(target.sequences, output = NULL, overwrite.dir = FALSE,
      control.sequences = NULL, weights = NULL, text = FALSE, brief = 1000,
      objfun = "classic", test = NULL, use_llr = FALSE, shuf = 2,
      hsfrac = NULL, cefrac = NULL, searchsize = NULL, norand = FALSE,
      csites = 1000, seed = 0, alph = NULL, revcomp = FALSE, pal = FALSE,
      mod = "zoops", nmotifs = 3, evt = NULL, nsites = NULL,
      minsites = NULL, maxsites = NULL, wnsites = 0.8, w = NULL,
      minw = 8, maxw = 50, allw = NULL, nomatrim = FALSE, wg = 11,
      ws = 1, noendgaps = FALSE, bfile = NULL, markov_order = 0,
      psp = NULL, maxiter = 50, distance = 0.001, prior = NULL, b = NULL,
      plib = NULL, spfuzz = NULL, spmap = NULL, cons = NULL, p = NULL,
      maxsize = NULL, maxtime = NULL, wd = getwd(), logfile = paste0(wd,
      "/memerun.log"), readsites = TRUE, echo = FALSE, verbose = 1,
      timeout = Inf, bin = getOption("meme.bin"))

### Arguments

`target.sequences` | `XStringSet` List of sequences to get motifs from.
`output` | `character(1)` Name of the output folder. If `NULL`, MEME output will be deleted.
`overwrite.dir` | `logical(1)` If `output` is set but already exists, allow over-writing.
`control.sequences` | `XStringSet` List of negative sequences. Only used if `objfun = c("de", "se")`.
`weights` | `numeric` Vector of numbers between 0 and 1, representing sequence weights.
`text` | `logical(1)` [MEME]
`brief` | `numeric(1)` [MEME]
`objfun` | `character(1)` [MEME]
`test` | `character(1)` [MEME]
`use_llr` | `logical(1)` [MEME]
`shuf` | `numeric(1)` [MEME]
`hsfrac` | `numeric(1)` [MEME]
`cefrac` | `numeric(1)` [MEME]
`searchsize` | `numeric(1)` [MEME]
`norand` | `logical(1)` [MEME]
`csites` | `numeric(1)` [MEME]
`seed` | `numeric(1)` [MEME]
`alph` | `character(1)` [MEME]
`revcomp` | `logical(1)` [MEME]
`pal` | `logical(1)` [MEME]
`mod` | `character(1)` [MEME]
`nmotifs` | `numeric(1)` [MEME]
`evt` | `numeric(1)` [MEME]
`nsites` | `numeric(1)` [MEME]
`minsites` | `numeric(1)` [MEME]
`maxsites` | `numeric(1)` [MEME]
`wnsites` | `numeric(1)` [MEME]
`w` | `numeric(1)` [MEME]
`minw` | `numeric(1)` [MEME]
`maxw` | `numeric(1)` [MEME]
`allw` | `numeric(1)` [MEME]
`nomatrim` | `logical(1)` [MEME]
`wg` | `numeric(1)` [MEME]
`ws` | `numeric(1)` [MEME]
`noendgaps` | `logical(1)` [MEME]
`bfile` | `character(1)` [MEME]
`markov_order` | `numeric(1)` [MEME]
`psp` | `character(1)` [MEME]
`maxiter` | `numeric(1)` [MEME]
`distance` | `numeric(1)` [MEME]
`prior` | `character(1)` [MEME]
`b` | `numeric(1)` [MEME]
`plib` | `character(1)` [MEME]
`spfuzz` | `numeric(1)` [MEME]
`spmap` | `character(1)` [MEME]
`cons` | `character(1)` [MEME]
`p` | `numeric(1)` [MEME]
`maxsize` | `numeric(1)` [MEME]
`maxtime` | `numeric(1)` [MEME]
`wd` | `character(1)` Working directory to run MEME in.
`logfile` | `character(1)` File to dump MEME stderr. If `NULL`, no logs will be saved.
`readsites` | `logical(1)` Read sites from MEME output (from `read_meme()`).
`echo` | `logical(1)` Dump MEME output to console.
`verbose` | `numeric(1)` Set `verbose = 0` to quiet `run_meme()`.
`timeout` | `numeric(1)` Stop MEME program past `timeout` (seconds). See `processx::run()`.
`bin` | `character(1)` Location of MEME binary. Alternatively, set this via `options(meme.bin = '/path/to/meme/bin')`.

### Value

`list` The output file is read with `read_meme()`.

### Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

### References

Bailey TL, Elkan C (1994). “Fitting a mixture model by expectation maximization to discover motifs in biopolymers.” Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 2, 28-36.

### See Also

`read_meme()`, `create_sequences()`, `shuffle_sequences()`, `processx::run()`

### Examples

    ## Not run:
    ## To check that you are properly linking to the binary:
    run_meme()

    ## End(Not run)

[Package universalmotif version 1.10.2 Index]