SEC/GPC Integration Window

step_sec_integration_window() creates a specification of a recipe step that defines the integration window (start and end x-axis bounds) for molecular weight calculations. This step adds an .integration_window column that downstream steps like step_sec_mw_averages() can use.

Usage

step_sec_integration_window(
  recipe,
  measures = NULL,
  start = NULL,
  end = NULL,
  auto_detect = TRUE,
  signal_threshold = 0.01,
  extend_beyond_cal = 0.5,
  calibration_range = NULL,
  min_window_width = 1,
  role = NA,
  trained = FALSE,
  skip = FALSE,
  id = recipes::rand_id("sec_integration_window")
)

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.
start: Numeric. Start of integration window (x-axis value, e.g., mL). If NULL and auto_detect = TRUE, determined automatically from data.
end: Numeric. End of integration window (x-axis value, e.g., mL). If NULL and auto_detect = TRUE, determined automatically from data.
auto_detect: Logical. If TRUE (default), automatically determine window bounds from the data when start or end is NULL.
signal_threshold: Numeric between 0 and 1. When auto-detecting, the fraction of maximum signal to use as threshold for defining significant signal region. Default is 0.01 (1% of max).
extend_beyond_cal: Numeric. Fraction of calibration range to extend beyond the maximum calibration point for capturing low MW species. Default is 0.5 (50% extension). Only used when calibration info is available via calibration_range.
calibration_range: Optional numeric vector c(min, max) specifying the calibration range in x-axis units. When provided, auto-detection respects these bounds and applies extend_beyond_cal.
min_window_width: Numeric. Minimum window width to ensure valid integration. Default is 1.0 (1 mL for SEC).
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 .integration_window column will be added containing a tibble with start and end for each sample.

Details

The integration window defines the x-axis region used for molecular weight calculations. For SEC/GPC, this typically corresponds to elution volume.

Auto-detection algorithm:

Find significant signal region (above signal_threshold of max)
Extend slightly beyond signal boundaries
If calibration_range provided, constrain start to calibration minimum
Allow extension up to extend_beyond_cal beyond calibration maximum to capture low MW species
Ensure minimum window width

Output format: The .integration_window column contains a list of tibbles, one per row, each with columns:

start: Start of integration window
end: End of integration window

Tidying

When you tidy() this step, a tibble with columns terms, start, end, auto_detect, and id is returned.

Examples

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

# Auto-detect integration window
rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_integration_window() |>
  prep()

# Explicit window bounds
rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_integration_window(start = 8.0, end = 18.0) |>
  prep()

# With calibration constraints
rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri_signal, location = vars(elution_volume)) |>
  step_sec_integration_window(
    calibration_range = c(9.0, 16.0),
    extend_beyond_cal = 0.5
  ) |>
  prep()
} # }