Fetch problematic peak mappings

Fetch peak mappings that were problematic in any way (from iso_files or directly from a peak_table). This function is typically called after iso_map_peaks to inspect problematic entries. Use the select parameter to select only the most informative columns (always includes at minimum the peak_info and problem columns to identify why the peak is problematic). Note that peaks that are ambiguous because of multiple potential map matches have a data table entry for each potential match.

iso_get_problematic_peak_mappings(...)

# S3 method for iso_file_list
iso_get_problematic_peak_mappings(
  iso_files,
  select = everything(),
  include_file_info = NULL,
  unidentified = TRUE,
  missing = TRUE,
  ambiguous = TRUE,
  quiet = default(quiet)
)

# S3 method for data.frame
iso_get_problematic_peak_mappings(
  peak_table,
  select = everything(),
  unidentified = TRUE,
  missing = TRUE,
  ambiguous = 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
select	which column to select, by default all
include_file_info	which file information to include (see iso_get_file_info). Use c(...) to select multiple, supports all select syntax including renaming columns.
unidentified	whether to include peaks that are problematics because they are unidentified
missing	whether to include peaks that are problematics because they are missing
ambiguous	whether to include peaks that are problematics because they are ambiguously identified
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.

Value

data table with rows for problematic peaks and the select-identified columns