process_corecmotifs: Filter a list of CoRecMotifs and match them to reference...
In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

process_corecmotifs

R Documentation

Filter a list of CoRecMotifs and match them to reference motifs

Description

Removes CoRecMotifs with low z-scores or motif strengths and CoRecMotifs that do not replicate, then compares the remaining CoRecMotifs to a database of reference motifs to identify the best match. This is a convenience function that calls filter_corecmotifs(), check_replicates(), find_match(), then filter_corecmotifs() and check_replicates() again, and finally summarize_corecmotifs() and optionally compare_conditions().

Usage

process_corecmotifs(
  corecmotifs,
  reference_motifs_file,
  cluster_assignments = NULL,
  meme_path = NULL,
  motif_strength = 1,
  rolling_ic = 1,
  n_replicates = 2,
  eucl_distance = 0.4,
  min_overlap = 5,
  match_pvalue = 0.01,
  pbm_condition_groups = NULL,
  output_directory = NULL,
  output_base_name = NULL
)

Arguments

`corecmotifs`	`list`. The CoRecMotifs to process.
`reference_motifs_file`	`character(1)`. The path to the MEME format file of reference motifs to match to.
`cluster_assignments`	`data.frame` or `NULL`. A table mapping the reference motifs to motif clusters or NULL to skip the cluster assignment step. See motif_clusters for expected columns. (Default: NULL)
`meme_path`	`character(1)` or `NULL`. The path to "meme/bin/" or NULL to rely on `memes::runTomTom()` to find it. (Default: NULL)
`motif_strength`	`numeric(1)` or `NULL`. The minimum motif strength to keep or NULL not to filter by motif strength. (Default: 1)
`rolling_ic`	`numeric(1)` or `NULL`. The minimum rolling IC to keep or NULL not to filter by rolling IC. (Default: 1)
`n_replicates`	`integer(1)`. The minimum number of replicates to require. Set this to 1 to skip filtering by number of replicates. (Default: 2)
`eucl_distance`	`numeric(1)` or `NULL`. The maximum allowable Euclidean distance between replicate motifs or NULL to skip the replicate comparison step. (Default: 0.4)
`min_overlap`	`integer(1)`. The minimum amount of overlap to require when comparing a CoRecMotif to a reference motif. (Default: 5)
`match_pvalue`	`numeric(1)` or `NULL`. The maximum match p-value to keep or NULL not to filter by match p-value. (Default: 0.01)
`pbm_condition_groups`	`list(character)` or `NULL`. The names of the PBM conditions to compare. Each element of the list should contain a group of PBM conditions to compare to each other. If the list elements are named, the names will be passed to the `group_name` parameter of `compare_conditions()`. (Default: NULL)
`output_directory`	`character(1)` or `NULL`. The path to the directory where output files will be saved. No output files will be created unless `output_directory` or `output_base_name` is provided. (Default: NULL)
`output_base_name`	`character(1)` or `NULL`. The base name for output files. No output files will be created unless `output_directory` or `output_base_name` is provided. (Default: NULL)

Details

By default no output files are created. To save output files, you must provide output_directory, output_base_name, or both. The output files are named according to the following rules.

If output_directory is provided but output_base_name is not, the files will be saved in the provided directory using the base name "output".
If output_base_name is provided but output_directory is not, the files will be saved in the working directory using the provided base name.
The individual output file names will be identified by a suffix appended to the output base name.
The output after the first call to filter_corecmotifs() and check_replicates() will have the suffix "filtered_corecmotifs.rds".
The output of find_match() will have the suffix "matched_corecmotifs.rds".
The output after the second call to filter_corecmotifs() and check_replicates() will have the suffix "significant_corecmotifs.rds".
The output of summarize_corecmotifs() will have the suffix "significant_corecmotifs_summary.tsv".
The output of summarize_corecmotifs() with by_cluster = TRUE will have the suffix "significant_corecmotifs_summary_by_cluster.tsv".
The output of compare_conditions() will have the suffix "condition_comparisons.tsv".