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.

### 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.

### 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, b2tremblay@uwaterloo.ca

### References

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.

### 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"))

[Package universalmotif version 1.2.1 Index]