Correct declared (custom) interferences

Applies the interference corrections you declared in the feature metadata (the legacy interference_feature_id / interference_contribution columns, and any source == "manual" rows in annot_interferences) to the raw feature intensities, using the same engine and formula as correct_isotopic_interferences(). Use this for in-source fragments, co-eluting isobars or other non-isotopic interferences you know about. Warns and returns the data unchanged if none are defined.

Usage

correct_custom_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.

See also

correct_isotopic_interferences(), correct_interference_manual(); the interference-correction guide.