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

read_denovo_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:

  • consensus the consensus sequence of the denovo motif

  • motif_name name of the motif

  • log_odds_detection threshold used to determine bound vs. unbound sites

  • motif_pwm a list column with PWMs for each motif

  • log_p_value_detection from the original experiment used to ID motif

  • 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

  • log_p_value final enrichment from experiment -log10(p-value)

  • tgt_pos average position of motif in target sequences, where 0 = start of sequences

  • tgt_std standard deviation of position in target sequences

  • bgd_pos average position of motif in background sequences, where 0 = start of sequences

  • bgd_std standard deviation of position in background sequences

  • strand_bias log ratio of + strand occurrences to - strand occurrences

  • multiplicity average number of occurrences per sequence in sequences with 1 or more binding sites

Details

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

See also

read_known_results, find_motifs_genome