Reads in results from a known motif enrichment analysis created by HOMER.

read_known_results(path, homer_dir = TRUE)

Arguments

path

path to the HOMER directory where all outputs are stored

homer_dir

does the path point to a HOMER directory; if FALSE, path must point to the file directly [default: TRUE]

Value

a tibble with the following columns:

  • motif_name the readable name of the sequence

  • motif_family of transcription factors the motif belongs to

  • experiment from where the motif was identified

  • accession source publication or online repository ID

  • database the curator of the motif

  • consensus the accepted consensus motif sequence

  • log_p_value -log10(p-value) significance of enrichment

  • fdr Benjamini-Hochberg corrected p-value

  • tgt_num number of times motif appears in target sequences

  • tgt_pct percent of times motif appears in target sequences

  • bgd_num number of times motif appears in background sequences

  • bgd_pct percent of times motif appears in background sequences

Details

Following an analysis using find_motifs_genome, a HOMER directory is created which analyses the enrichment of known motifs. This function reads and parses in that file into a tidy format.

See also

read_denovo_results, find_motifs_genome