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. 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)

### 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.

### 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.

### Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

### 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"])

[Package universalmotif version 1.10.2 Index]