Find similar motifs

Search through provided motif database to find similar motifs to the input. Light wrapper around TOMTOM from MEME Suite.

Usage

find_motifs(
  streme_out,
  motif_db,
  out_dir = tempdir(),
  meme_path = NULL,
  BPPARAM = BiocParallel::bpparam(),
  verbose = FALSE,
  debug = FALSE,
  ...
)

Arguments

streme_out

Output from denovo_motifs.

motif_db

Path to .meme format file to use as reference database, or a list of universalmotif-class objects. (optional) Results from de-novo motif discovery are searched against this database to find similar motifs. If not provided, JASPAR CORE database will be used. NOTE: p-value estimates are inaccurate when the database has fewer than 50 entries.

out_dir

A character vector of output directory to save STREME results to. (default = tempdir())

meme_path

path to "meme/bin/" (default: NULL). Will use default search behavior as described in check_meme_install() if unset.

BPPARAM

A BiocParallelParam-class object specifying run parameters. (default = bpparam())

verbose

A logical indicating whether to print verbose messages while running the function. (default = FALSE)

debug

A logical indicating whether to print debug messages while running the function. (default = FALSE)

...

Additional arguments to pass to TOMTOM. For more information, refer to the official MEME Suite documentation on TOMTOM.

Value

data.frame of match results. Contains best_match_motif column of universalmotif objects with the matched PWM from the database, a series of best_match_* columns describing the TomTom results of the match, and a tomtom list column storing the ranked list of possible matches to each motif. If a universalmotif data.frame is used as input, these columns are appended to the data.frame. If no matches are returned, tomtom and best_match_motif columns will be set to NA and a message indicating this will print.

Examples

if (memes::meme_is_installed()) {
    data("CTCF_TIP_peaks", package = "MotifPeeker")
    
    if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
        genome_build <-
            BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
   
        res <- denovo_motifs(list(CTCF_TIP_peaks),
                        trim_seq_width = 50,
                        genome_build = genome_build,
                        discover_motifs_count = 1,
                        filter_n = 10,
                        out_dir = tempdir())
        res2 <- find_motifs(res, motif_db = get_JASPARCORE(),
                            out_dir = tempdir())
        print(res2)
    }
}
#> Warning: p-values will be inaccurate if primary and control
#> Warning: p-values will be inaccurate if primary and control
#> [[1]]
#> [[1]][[1]]
#>          motif           name  altname  consensus alphabet strand  icscore
#> 1 <mot:m01_..> m01_TCCCAGCACD STREME-1 TCCCAKMACN      DNA     +- 11.51542
#>   nsites pval type pseudocount          bkg best_match_name best_match_altname
#> 1     21    1  PCM           0 0.24, 0.....        MA2125.1             Zfp809
#>                                              best_db_name best_match_offset
#> 1 6bb110a2b35_JASPAR2024_CORE_non-redundant_pfms_meme.txt                 1
#>   best_match_pval best_match_eval best_match_qval best_match_strand
#> 1         3.6e-05          0.0845           0.169                 +
#>   best_match_motif       tomtom
#> 1     <mot:MA21..> c("MA212....
#> 
#> [Hidden empty columns: family, organism, bkgsites, qval, eval.]
#> 
#>