read_denovo_results: Read Denovo Enriched Motifs HOMER Output

In robertamezquita/marge: API for HOMER in R for Genomic Analysis using Tidy Conventions

Description

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

Usage

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]

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.

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

See Also

read_known_results, find_motifs_genome

robertamezquita/marge documentation built on Sept. 30, 2020, 6:15 a.m.