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. DREME and STREME motifs can also be imported, but note
that readsites
and readsites.meta
arguments do nothing.
read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE)
file |
|
skip |
|
readsites |
|
readsites.meta |
|
Please note that the typical number precision limit in R is around 1e-308.
This means that motif P-values in MEME files below this limit are rounded
automatically to 0. To get around this, the E-value is also stored as a
string in the extrainfo
slot. If you require a numeric value for analysis,
use the log_string_pval()
function to get the log of the string-formatted
p-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.
Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca
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.
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")) ## Get numeric p-value: log_string_pval(meme.minimal[[1]]["extrainfo"]["eval.string"])