Update Annotation Table in a mass_dataset Object — mutate_annotation

This function updates the annotation table in a mass_dataset object by appending new annotation data and retaining only the top annotations based on the total score.

Usage

mutate_annotation_table(object, annotation_table)

Arguments

object: A mass_dataset object containing the existing annotation table.
annotation_table: A data frame containing new annotation data to be added to the mass_dataset object. The table should contain specific columns as detailed below.

Value

The function returns the updated mass_dataset object with the appended and processed annotation table.

Details

This function allows you to update or append new annotations to the existing annotation table in a mass_dataset object. The function ensures that the new annotations are properly arranged based on the Total.score, and it retains only the top annotations for each variable_id based on the specified candidate.num.

The annotation_table must contain the following columns:

variable_id: The unique identifier for each variable.
ms2_files_id: The ID of the MS2 file associated with each annotation.
ms2_spectrum_id: The ID of the MS2 spectrum associated with each annotation.
Compound.name: The name of the annotated compound.
CAS.ID: The CAS ID of the compound.
HMDB.ID: The HMDB ID of the compound.
KEGG.ID: The KEGG ID of the compound.
Lab.ID: The lab identifier for the compound.
Adduct: The adduct form of the compound.
mz.error: The error in m/z matching.
mz.match.score: The score for the m/z match.
RT.error: The error in retention time matching.
RT.match.score: The score for the retention time match.
CE: Collision energy used in MS2 matching.
SS: Spectral similarity score for MS2 matching.
Total.score: The total score for the annotation.
Database: The database used for annotation.
Level: The confidence level of the annotation.

Examples

if (FALSE) { # \dontrun{
# Example usage
updated_object <- mutate_annotation_table(
  object = my_dataset,
  annotation_table = new_annotation_data
)
} # }