Description Usage Arguments Value
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | iso_get_problematic_peak_mappings(...)
## S3 method for class '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 class 'data.frame'
iso_get_problematic_peak_mappings(
peak_table,
select = everything(),
unidentified = TRUE,
missing = TRUE,
ambiguous = TRUE,
quiet = default(quiet)
)
|
... |
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 |
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 |
data table with rows for problematic peaks and the select
-identified columns
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