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