read_meme: Import MEME motifs.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

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. DREME and STREME motifs can also be imported, but note that readsites and readsites.meta arguments do nothing.

Usage

read_meme(file, skip = 0, readsites = FALSE, readsites.meta = FALSE,
  readsites.meta.tidy = 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.
readsites.meta.tidy	logical(1) If readsites.meta = TRUE, merge the position site information for all motifs into a single tidy data.frame.

Details

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.

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. If readsites.meta.tidy = TRUE, an additional list entry named sites.meta.tidy will be added containing a data.frame.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

References

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.

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"))
## Get numeric p-value:
log_string_pval(meme.minimal[[1]]["extrainfo"]["eval.string"])

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.