Filter SIRIUS structure (CSI:FingerID) annotations by COSMIC confidence score

Applies a minimum COSMIC confidence cutoff to SIRIUS structure predictions inside an ecomet mmo object. The function reads a chosen annotation table from mmo[[input]] (default "sirius_annot"), flags structure annotations below threshold by setting selected structure-identification fields to NA, and stores the result as a new element on mmo named "sirius_annot_filtered_<suffix>".

Usage

filter_cosmic_structure(
  mmo,
  input = "sirius_annot",
  cosmic_mode = c("exact", "approx"),
  threshold = 0.5,
  fields = "auto",
  na_cosmic = TRUE,
  suffix = NULL,
  overwrite = FALSE,
  verbose = TRUE
)

Arguments

mmo: An ecomet mmo object containing mmo[[input]] (a data.frame).
input: Character. Name of the element on mmo to filter. Defaults to "sirius_annot".
cosmic_mode: Which COSMIC column to use. One of "exact" or "approx".
threshold: Numeric. Keep structures with COSMIC >= threshold.
fields: Character vector of columns to NA-out when COSMIC < threshold. If "auto" (default), uses a reasonable default set if present in the table.
na_cosmic: Logical. If TRUE (default), also set the COSMIC value to NA when the structure is filtered out.
suffix: Optional character string appended to the created element name.
overwrite: Logical. If FALSE (default) and the target element already exists, error.
verbose: Logical. If TRUE, prints a concise summary.

Value

The updated mmo object, with a new element mmo[[paste0("sirius_annot_filtered_", suffix)]].

Details

Rows are never dropped. "Removing" a structure means setting selected fields (e.g., SMILES/InChI/name/InChIkey2D) to NA.

Examples

if (FALSE) { # \dontrun{
mmo <- filter_cosmic_structure(mmo, input = "sirius_annot",
                              cosmic_mode = "approx", threshold = 0.5,
                              suffix = "COSMIC_exact_0.5", verbose = TRUE)
} # }