read_meme: Import MEME motifs.
In universalmotif: Import, Modify, and Export Motifs with R

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE)

`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.

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, b2tremblay@uwaterloo.ca

\insertRef

memeuniversalmotif

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"])