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Identify isotopocules

Source: R/mapping.R
orbi_identify_isotopocules.Rd

Map the mass spectral peaks to specific isotopocules based on their mass.

Usage

orbi_identify_isotopocules(
  aggregated_data,
  isotopocules,
  default_tolerance = 1,
  default_charge = 1
)

Arguments

aggregated_data

either data aggregated from orbi_aggregate_raw() or a straight-up tibble data frame of the peaks (e.g. retrieved via orbi_get_data(peaks = everything())).

isotopocules

list of isotopocules to map, can be a data frame/tibble, a named vector such as c("M0" = 61.9878, "15N" = 62.9850), or the name of a file to read from (.csv/.tsv/.xlsx are all supported). If provided as a tibble/file, the required columns are isotopocule/isotopolog and mz/mass (these alternative names for the columns, including uppercase versions, are recognized automatically). In addition, tolerance/tolerance [mmu]/tolerance [mDa], charge/z, #compound/compound, and fragment are recognized, as well as any other (arbitrarily named) columns with additional information. Character columns in the isotopocules table (including isotopocule and compound) are turned into factors with levels that preserve the order of isotopocules. That means that to change the order of isotopocules in downstream plotting functions, make sure to list them in the order you'd like them presented in. Note that if tolerance/tolerance [mmu]/tolerance [mDa] or charge/z are not provided, the values in the parameters default_tolerance and default_charge are used, respectively.

default_tolerance

tolerance (in mmu) to be used for isotopocule identification if a tolerance/tolerance [mmu]/tolerance [mDa] column is not included in isotopocules

default_charge

charge to be used for any unidentified peak, and if a charge/z column is not included in isotopocules

Value

same object as provided in aggregated_data with added columns compound (if provided), itc_uidx (introduced unique isotopocule index), isotopocule, mzExact, charge, and ions.incremental (via orbi_calculate_ions()), as as well as any other additional information columns provided in isotopocules. Note that if the default CN and RN values of orbi_calculate_ions() are not the ones that should be used, simply run orbi_calculate_ions() explicitly afterwards. Also note that the information about columns that were NOT aggregated in previous steps is purposefully not preserved at this step.