read_denovo_html_results: Read de novo enriched motifs from HOMER .info.html output...

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

Description

Reads in results from all individual info.html files produced by HOMER de novo motif enrichment analysis.

Usage

read_denovo_html_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 the .html file into a tidy format.

It might be more useful to read in the .html files instead of the .motifs file because the .html contain information on known similar motifs.

Value

a list with the following structure:

• Motif_information a dataframe with most of the info returned by read_denovo_results

• Matches_to_known_motifs Dataframe with information on related known motifs matched to the de novo motif

The Motif_information dataframe has the following columns:

• motif_name name of the motif

• consensus the consensus sequence of the denovo motif

• p_value final enrichment from experiment (p-value)

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

• info_content information Content per bp

• 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

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

• bgd_pos average position of motif in background sequences

• strand_bias strand Bias (log2 ratio + to - strand density)

• multiplicity multiplicity (# of sites on avg that occur together)

#' The Matches_to_known_motifs dataframe has the following columns:

• motif_name name of the motif

• motif_family family of the motif

• ID ID of the motif or the experiment

• database database of the motif

• rank match rank

• score log odds score of the motif matrix, higher scores are better matches

• offset from the center of the region

• orientation forward or reverse (on average?)

• original_alignment consensus sequence for comparison

• matched_alignment matched sequence with mismatches in "-" from the consensus. Can be offset.

#' @importFrom stringr str_replace str_split str_detect

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