Remove peak mappings that were problematic (unidentified, missing, or ambiguous) during peak mapping.

iso_remove_problematic_peak_mappings(...)

# S3 method for iso_file_list
iso_remove_problematic_peak_mappings(iso_files,
  remove_unidentified = TRUE, remove_missing = TRUE,
  remove_ambiguous = TRUE, remove_mapping_info_columns = TRUE,
  quiet = default(quiet))

# S3 method for data.frame
iso_remove_problematic_peak_mappings(peak_table,
  remove_unidentified = TRUE, remove_missing = TRUE,
  remove_ambiguous = TRUE, remove_mapping_info_columns = TRUE,
  quiet = default(quiet))

Arguments

...

S3 method placeholder parameters, see class specific functions for details on parameters

iso_files

collection of continuous flow iso_file objects

quiet

whether to display (quiet=FALSE) or silence (quiet = TRUE) information messages. Set parameter to overwrite global defaults for this function or set global defaults with calls to iso_turn_info_message_on and iso_turn_info_message_off

peak_table

data frame with mapped peaks. Requires the is_identified, is_missing and is_ambiguous columns to be present.

remove_mapping_info_column

whether to automatically remove mapping info columns. If true and:

  • remove_unidentified = TRUE - is_identified column automatically removed

  • remove_missing = TRUE - is_missing column automatically removed

  • remove_ambiguous = TRUE - is_ambiguous, n_matches, and n_overlapping columns automatically removed

Value

the data with the problematic peak mappings remove

See also