read_denovo_results.RdReads in results from a denovo motif enrichment analysis created by HOMER.
read_denovo_results(path, homer_dir = TRUE)
| path | path to the HOMER directory where all outputs are stored |
|---|---|
| homer_dir | does the path point to a HOMER directory;
if |
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
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.