run_meme: Run MEME from within R.

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/run_meme.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, run run_meme(). Parameters in run_meme() which are directly taken from the MEME program are tagged with [MEME]. This functions requires that the processx package be installed separately.

Usage

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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-writting.

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, b2tremblay@uwaterloo.ca

References

\insertRef

meme3universalmotif

See Also

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

Examples

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

## End(Not run)

universalmotif documentation built on April 8, 2021, 6 p.m.