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, readsites.meta = 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.

readsites.meta

logical(1) If readsites = TRUE, then additionally read site positions and P-values.

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. If readsites.meta = TRUE, then two additional list items will be present, one containing site positions and P-values, and another containing combined sequence p-values.

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 1.2.0 Index]