read_meme {universalmotif} | R Documentation |
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.
read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE)
file |
|
skip |
|
readsites |
|
readsites.meta |
|
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.
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
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.
Other read_motifs: read_cisbp
,
read_homer
, read_jaspar
,
read_matrix
, read_motifs
,
read_transfac
, read_uniprobe
meme.minimal <- read_meme(system.file("extdata", "meme_minimal.txt", package = "universalmotif")) meme.full <- read_meme(system.file("extdata", "meme_full.txt", package = "universalmotif"))