check_replicates: Check reproducibility of a list of CoRecMotifs
In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

check_replicates

R Documentation

Check reproducibility of a list of CoRecMotifs

Description

Filter a list of CoRecMotifs based on whether they are reproducible, i.e., found in multiple replicate experiments.

Usage

check_replicates(
  corecmotifs,
  n_replicates = 2,
  eucl_distance = 0.4,
  output_file = NULL,
  check_corecmotifs = TRUE
)

Arguments

`corecmotifs`	`list`. The CoRecMotifs to filter.
`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)
`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

This function is intended to be used in concert with filter_corecmotifs(). For example, you may want to remove any PBM condition/probe set combination that does not have at least 3 replicate CoRecMotifs with a motif strength of at least 1. In this case you would use filter_corecmotifs() with motif_strength = 1 to remove individual CoRecMotifs with low motif strengths followed by check_replicates() with n_replicates = 3 to remove any replicate groups that have fewer than 3 remaining CoRecMotifs.