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Correct automatically derived isotopic interferences

Source: R/correct-isotope.R
correct_isotopic_interferences.Rd

Applies the isotopic (M+2) interference corrections previously discovered by calc_isotopic_interferences() (and any declared interferences, see correct_custom_interferences()) to the raw feature intensities. Aborts with guidance if no interferences have been derived yet.

The subtraction is $$value_{corrected} = value_{raw} - K \cdot value_{interferer}$$ applied on the raw feature_intensity. For auto-derived (source == "auto") edges the interferer is clamped at 0 before subtraction and the result clamped at 0 (LICAR parity); declared ("manual") edges are unclamped. See calc_isotopic_interferences() for how K is computed.

A chain (e.g. PC 34:2 > PC 34:1 > PC 34:0) is corrected sequentially by default, each feature using its already-corrected interferer; set sequential_correction = FALSE to correct each from the raw interferer. The raw signal is preserved in feature_intensity_orig, and the correction is idempotent (re-running restores from raw first).

Usage

correct_isotopic_interferences(
  data = NULL,
  variable = "feature_intensity",
  sequential_correction = TRUE,
  neg_to_na = FALSE
)

Arguments

data

MRMhubExperiment object.

variable

Name of the variable to correct. Only "feature_intensity" (the raw intensity) is supported. Default: "feature_intensity".

sequential_correction

Logical. If TRUE (default), a chain of interferences is corrected sequentially so each feature uses the already-corrected signal of its interferer (propagates along the chain). If FALSE, each feature is corrected from the raw interferer, without propagation.

neg_to_na

If TRUE, negative or zero values after correction are replaced with NA. Default: FALSE.

Value

MRMhubExperiment object with feature intensities corrected.

References

Gao L., Ji S, Burla B, Wenk MR, Torta F, & Cazenave-Gassiot A (2021). LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring. Analytical Chemistry, 93(6), 3163-3171. https://doi.org/10.1021/acs.analchem.0c04565

See also

The interference-correction guide.