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Filter CANOPUS / SIRIUS annotations in an ecomet mmo object by probability threshold

filter_canopus_annotations.Rd

Applies a minimum-probability cutoff to selected CANOPUS (NPClassifier / ClassyFire) annotation levels inside an ecomet mmo object. The function reads a chosen annotation table from mmo[[input]] (default "sirius_annot"), flags annotations below threshold by setting them to NA, and stores the result as a new element on mmo named "sirius_annot_filtered_<suffix>".

Usage

filter_canopus_annotations(
  mmo,
  input = "sirius_annot",
  pathway_level = "NPC#pathway",
  threshold = 0.9,
  na_prob = 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".

pathway_level

Character vector of one or more annotation header(s) to filter. Valid options include:

  • "All"

  • "All_NPC"

  • "All_ClassyFire"

  • "NPC#pathway"

  • "NPC#superclass"

  • "NPC#class"

  • "ClassyFire#superclass"

  • "ClassyFire#class"

  • "ClassyFire#subclass"

  • "ClassyFire#level 5"

  • "ClassyFire#most specific class"

Special values:

  • "All" expands to all NPC + ClassyFire levels listed above.

  • "All_NPC" expands to NPC levels only.

  • "All_ClassyFire" expands to ClassyFire levels only.

threshold

Decimal between 0 and 1. Annotations with probability < threshold are flagged to NA.

na_prob

Logical. If TRUE (default), also set the corresponding probability value to NA.

suffix

Optional character string appended to the created element name: "sirius_annot_filtered_<suffix>". If NULL (default), a suffix is auto-generated.

overwrite

Logical. If FALSE (default) and the target element already exists on mmo, the function errors to avoid accidental overwrites.

verbose

Logical. If TRUE, prints a concise summary including counts of non-missing annotations before and after filtering.

Value

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

Details

Rows are never dropped. "Removing" an annotation means setting the annotation value (and optionally its probability column) to NA.

For each annotation column (e.g., "NPC#pathway"), the function looks for an associated probability column using common SIRIUS export naming:

  • "<header> Probability"

  • "<header> probability"

  • "<header>Probability"

Examples

if (FALSE) { # \dontrun{
mmo <- filter_canopus_annotations(mmo, input = "sirius_annot",
                                 pathway_level = "NPC#pathway", threshold = 0.9,
                                 suffix = "NPC_pathway_0.9", verbose = TRUE)

mmo <- filter_canopus_annotations(mmo, input = "sirius_annot_filtered_NPC_pathway_0.9",
                                 pathway_level = "All_NPC", threshold = 0.95,
                                 suffix = "All_NPC_0.95", verbose = TRUE)
} # }