write_meme: Export motifs in MEME format.

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

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, [e-mail]

References

Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009). “MEME SUITE: tools for motif discovery and searching.” Nucleic Acids Research, 37, W202-W208.

See Also

read_meme()

Other write_motifs: write_homer(), write_jaspar(), write_matrix(), write_motifs(), write_transfac()

Examples

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

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.