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SEC/GPC Region Exclusion

Source: R/step_sec_exclude_regions.R
step_sec_exclude_regions.Rd

step_sec_exclude_regions() creates a specification of a recipe step that marks regions for exclusion from analysis. Excluded regions can be solvent peaks, artifacts, flow markers, or other features that should not be included in baseline fitting or molecular weight integration.

Usage

step_sec_exclude_regions(
  recipe,
  measures = NULL,
  regions = NULL,
  purpose = c("both", "baseline", "integration"),
  role = NA,
  trained = FALSE,
  skip = FALSE,
  id = recipes::rand_id("sec_exclude_regions")
)

Arguments

recipe

A recipe object. The step will be added to the sequence of operations for this recipe.

measures

An optional character vector of measure column names to process. If NULL (the default), all measure columns will be processed.

regions

A data frame or tibble specifying regions to exclude. Must contain columns start and end (x-axis values defining each region). Optional columns: reason (character describing why excluded), sample_id (for sample-specific exclusions).

purpose

Character. What the exclusions apply to:

  • "baseline": Exclude from baseline fitting only

  • "integration": Exclude from MW integration only

  • "both" (default): Exclude from both baseline fitting and integration

role

Not used by this step since no new variables are created.

trained

A logical to indicate if the quantities for preprocessing have been estimated.

skip

A logical. Should the step be skipped when the recipe is baked?

id

A character string that is unique to this step to identify it.

Value

An updated version of recipe with the new step added to the sequence of any existing operations. An .excluded_regions column will be added containing exclusion information for each sample.

Details

Excluded regions are stored in a list column .excluded_regions where each element is a tibble with columns:

  • start: Start of excluded region (x-axis value)

  • end: End of excluded region (x-axis value)

  • purpose: What this exclusion applies to

  • reason: Optional description of why this region is excluded

Sample-specific exclusions: If the regions data frame includes a sample_id column, exclusions can be applied only to specific samples. Rows without sample_id (or with sample_id = NA) are applied globally to all samples.

Common uses:

  • Solvent peaks that elute at the end of the chromatogram

  • System peaks or artifacts at specific retention times

  • Flow marker peaks used for retention time correction

  • Air bubbles or other transient artifacts

Tidying

When you tidy() this step, a tibble with columns terms, n_regions, purpose, and id is returned.

See also

step_sec_baseline() which can use exclusion information, step_sec_mw_averages() which respects integration exclusions.

Other sec-chromatography: step_sec_band_broadening(), step_sec_baseline(), step_sec_detector_delay(), step_sec_integration_window(), step_sec_mw_averages(), step_sec_mw_distribution(), step_sec_mw_fractions(), step_sec_peaks_deconvolve(), step_sec_peaks_detect(), step_sec_peaks_refine()

Examples

if (FALSE) { # \dontrun{
library(recipes)
library(measure)

# Exclude a single region (solvent peak at end)
exclusions <- tibble::tibble(
  start = 18.5,
  end = 20.0,
  reason = "Solvent peak"
)

rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_exclude_regions(regions = exclusions) |>
  prep()

# Exclude multiple regions
exclusions <- tibble::tibble(
  start = c(8.0, 18.5),
  end = c(9.0, 20.0),
  reason = c("Void volume", "Solvent peak")
)

rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_exclude_regions(regions = exclusions, purpose = "integration") |>
  prep()

# Sample-specific exclusions
exclusions <- tibble::tibble(
  start = c(18.5, 15.0),
  end = c(20.0, 16.0),
  sample_id = c(NA, "sample_2"),  # NA = global, specific sample_id = per-sample
  reason = c("Solvent peak", "Artifact in sample_2")
)

rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_exclude_regions(regions = exclusions) |>
  prep()
} # }