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Calculate Analyte Concentrations Using Internal Standards

Source: R/calc-istd-normalization.R
quantify_by_istd.Rd

This function calculates analyte concentrations based on internal standard (ISTD) normalized intensities and the corresponding spiked-in ISTD amount, normalized by the sample amount.

Usage

quantify_by_istd(
  data = NULL,
  concentration_unit = "molar",
  ignore_missing_annotation = FALSE,
  ignore_istds = FALSE
)

Arguments

data

A MidarExperiment object

concentration_unit

Character string indicating the type of concentration to calculate and export. Must be either "molar" for molar concentrations (e.g., µmol/L) or "mass" for mass concentrations (e.g., µg/L).

ignore_missing_annotation

If FALSE, an error will be raised if any of the following information is missing: ISTD concentration, ISTD mix volume, and sample amounts for any feature. If TRUE, missing annotations will be ignored, and resulting feature concentration will be NA

ignore_istds

If TRUE, ISTD features will be ignored in the concentration calculation and the resulting concentration will be NA. Default is FALSE.

Value

A MidarExperiment object with the calculated analyte concentrations added to the dataset table in the feature_conc column.

Details

By default, concentrations are returned in molar units (e.g., µmol/L). To return concentrations in mass units (e.g., µg/L), set concentration_unit = "mass". This requires either the chemical formula or molecular weight for each feature to be specified in the feature metadata.

Internal standard concentrations can also be provided in ng/mL. In such cases, the function will convert these concentrations to molar units for internal calculations. Here too, either the chemical formula or the molecular weight must be defined for each ISTD in the feature metadata.

The unit of the calculated concentrations is determined by the concentration_unit argument and the sample_amount_unit field in the analysis metadata of the MidarExperiment object. The function will automatically adjust the sample amount to the appropriate unit based on the provided concentration_unit. For example, if concentration_unit = "molar" and sample_amount_unit = "uL", the calculated concentrations will be in µmol/L. If concentration_unit = "mass", the concentrations will be in µg/L.

The calculated concentrations are added to the dataset table as a new column named feature_conc..

See also

quantify_by_calibration() for calculating concentrations based on external calibration curves.