run_meme: Run MEME from within R.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

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] Note: custom alphabet definition files can be created using meme_alph().
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, [e-mail]

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)

bjmt/universalmotif documentation built on March 18, 2024, 8:32 a.m.