read_meme {universalmotif}R Documentation

Import MEME motifs.

Description

Import MEME formatted motifs, as well as original motif sequences. See http://meme-suite.org/doc/meme-format.html. Both 'full' and 'minimal' formats are supported.

Usage

read_meme(file, skip = 0, readsites = FALSE)

Arguments

file

character(1) File name.

skip

numeric(1) If not zero, will skip however many desired lines in the file before starting to read.

readsites

logical(1) If TRUE, the motif sites will be read as well.

Value

list universalmotif objects. If readsites = TRUE, a list comprising of a sub-list of motif objects and a sub-list of motif sites will be returned.

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.

See Also

Other read_motifs: read_cisbp, read_homer, read_jaspar, read_matrix, read_motifs, read_transfac, read_uniprobe

Examples

meme.minimal <- read_meme(system.file("extdata", "meme_minimal.txt",
                                      package = "universalmotif"))
meme.full <- read_meme(system.file("extdata", "meme_full.txt",
                                   package = "universalmotif"))


[Package universalmotif version 1.0.22 Index]