find_match: Match a list of CoRecMotifs to reference motifs
In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

find_match

R Documentation

Match a list of CoRecMotifs to reference motifs

Description

Identifies the reference motif that is the best match to each CoRecMotif.

Usage

find_match(
  corecmotifs,
  reference_motifs_file,
  cluster_assignments = NULL,
  meme_path = NULL,
  min_overlap = 5,
  output_file = NULL,
  check_corecmotifs = TRUE
)

Arguments

`corecmotifs`	`list`. The CoRecMotifs to match to reference motifs.
`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)
`min_overlap`	`integer(1)`. The minimum amount of overlap to require when comparing a CoRecMotif to a reference motif. (Default: 5)
`output_file`	`character(1)` or `NULL`. The path to the file where the results should be saved, or NULL not to save the results. (Default: NULL)
`check_corecmotifs`	`logical(1)`. Should `corecmotifs` be checked for validity? Setting this to FALSE can increase speed, but if `corecmotifs` contains anything other than valid CoRecMotifs, it may produce uninformative error messages. (Default: TRUE)

Details

The PPM representation of each CoRecMotif is compared to the reference motifs with memes::runTomTom() using Euclidean distance ("ed") as the distance metric. The match_motif and match_pvalue slots of the CoRecMotif are filled in based on the best match returned by memes::runTomTom(). The match_pvalue slot is corrected for multiple comparisons by multiplying the raw match p-value by the number of motifs in the reference database. The match_cluster slot is filled in based on the user-provided cluster assignments or left empty if no cluster assignments are provided.