This function flags isotopocules that are not detected in a minimum of min_percent of scans that then can be easily visualized with orbi_plot_isotopocule_coverage().
It evaluates weak isotopocules within each "uidx", "filename", "block", "segment" and "injection" (for those of the columns that exist),
in addition to any groupings already defined before calling this function using dplyr's group_by(). It restores the original groupings in the returned data.
Arguments
- dataset
A simplified IsoX data frame to be processed
- min_percent
A number between 0 and 100 (inclusive). Isotopocule must be observed in at least this percentage of scans (please note: the percentage is defined relative to the most commonly observed isotopocule of each compound). The default is 100, the most stringent condition to ensure reliable isotpocule coverage and ratio calculations across data blocks. If you lower the default, be mindful of potential misinterprations from using isotopotcules that are very close to their detection limit within a datablock. For continuous flow operations it may be necessary to make data blocks smaller using
orbi_define_block_for_flow_injection()andorbi_adjust_block().
Value
same object as provided in dataset with new column is_weak_isotopocule that flags weak isotopocules.
Examples
fpath <- system.file("extdata", "testfile_flow.isox", package = "isoorbi")
df <- orbi_read_isox(file = fpath) |>
orbi_simplify_isox() |>
orbi_flag_weak_isotopocules(min_percent = 100)
#> ✔ [21ms] orbi_read_isox() loaded 6449 peaks for 1 compound (HSO4-) with 5
#> isotopocules (M0, 33S, 17O, 34S, and 18O) from testfile_flow.isox
#> ✔ [5ms] orbi_simplify_isox() kept columns filepath, filename, scan.no,
#> time.min, compound, isotopocule, ions.incremental, tic, and it.ms
#> ✔ [34ms] orbi_flag_weak_isotopocules() flagged 1 of 15 isotopocules as weak
#> because they were NOT present in at least 100% of scans in each of the 15 data
#> groups (based on filename, compound, and isotopocule) → use
#> orbi_plot_isotopocule_coverage() to visualize them