R: Export motifs in MEME format.

write_meme {universalmotif}

R Documentation

Export motifs in MEME format.

Description

Convert motifs to minimal MEME format and write to file. See http://meme-suite.org/doc/meme-format.html.

Usage

write_meme(motifs, file, version = 5, bkg, strand, overwrite = FALSE,
  append = FALSE)

Arguments

`motifs`	See `convert_motifs()` for acceptable formats.
`file`	`character(1)` File name.
`version`	`numeric(1)` MEME version.
`bkg`	`numeric` Background letter frequencies. If missing, will use background frequencies from motif objects (if they are identical); else background frequencies will be set to freq = 1/length(alphabet)
`strand`	`character` If missing, will use strand from motif objects (if identical); otherwise will default to "+ -"
`overwrite`	`logical(1)` Overwrite existing file.
`append`	`logical(1)` Add to an existing file. Motifs will be written in minimal format, so it is recommended to only use this if the existing file is also a minimal MEME format file.

Value

NULL, invisibly.

Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

References

Bailey T, Boden M, Buske F, Frith M, Grant C, Clementi L, Ren J, Li W, Noble W (2009). “MEME SUITE: tools for motif discovery and searching.” Nucleic Acids Research, 37, W202-W208.

Examples

transfac <- read_transfac(system.file("extdata", "transfac.txt",
                                    package = "universalmotif"))
write_meme(transfac, tempfile())

[Package universalmotif version 1.5.36 Index]