importMeme: Import MEME results

In snystrom/dremeR: motif matching, comparison, and de novo discovery using the MEME Suite

Import MEME results

Description

This is a light wrapper around [universalmotif::read_meme()] that imports MEME results as universalmotif data.frame. If MEME is run with genomic coordinates in the fasta header, in "chr:start-end" format (base 1 indexed), the genomic coordinates of the motif match from input sequences can be parsed from the header.

Usage

importMeme(meme_txt, parse_genomic_coord = FALSE, combined_sites = FALSE)

Arguments

meme_txt	path to "meme.txt" output
parse_genomic_coord	whether to parse sequence headers into genomic coordinates for motif position information, only works if fasta files were written such that the sequence headers are in the form: "chr:start-end", or some variation of this form (delimiters can be any of: "[^[:alnum:]]+" (ie non-alphanumeric characters)), (default = FALSE).
combined_sites	whether to add 'combined_sites' output which contains coordinates of each sequence, the motif sequence (if 'parse_genomic_coord = TRUE'), and the 'diagram' column raw output from MEME indicating the relative locations of motifs in the sequence.

Value

MEME results in universalmotif data.frame format (see: [as_universalmotif_dataframe()]). 'sites_hits' is a nested data.frame column containing the position within each input sequence of matches to the identified motif.

See Also

[runMeme()] [universalmotif::read_meme()]

Examples

example_meme_txt <- system.file("extdata", "meme_full.txt", package = "universalmotif")
importMeme(example_meme_txt)

snystrom/dremeR documentation built on Oct. 13, 2024, 10:48 p.m.