read_known_results: Read Known Enriched Motifs HOMER output

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

Description

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

Usage

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]

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.

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

See Also

read_denovo_results, find_motifs_genome

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