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Flow Marker Correction for SEC/GPC

Source: R/step_sec_flow_marker.R
step_sec_flow_marker.Rd

step_sec_flow_marker() creates a specification of a recipe step that detects a flow marker peak (typically toluene or other small molecule) and applies a linear correction to align retention times/volumes across runs.

Usage

step_sec_flow_marker(
  recipe,
  measures = NULL,
  marker_range = NULL,
  target_volume = NULL,
  auto_detect = TRUE,
  min_peak_height = NULL,
  store_correction = TRUE,
  role = NA,
  trained = FALSE,
  skip = FALSE,
  id = recipes::rand_id("sec_flow_marker")
)

Arguments

recipe

A recipe object.

measures

Character vector of measure column names to correct. If NULL, uses all measure columns.

marker_range

Numeric vector of length 2 specifying the expected elution range c(min, max) where the flow marker peak is expected. Required unless auto_detect = TRUE with expected_volume specified.

target_volume

The target elution volume to align the flow marker to. If NULL (default), uses the first value of marker_range.

auto_detect

Logical. If TRUE, automatically detect the flow marker peak within marker_range. If FALSE, uses the peak maximum within range. Default is TRUE.

min_peak_height

Minimum peak height (in signal units) for a valid flow marker detection. Peaks below this threshold are ignored. Default is NULL (no minimum).

store_correction

Logical. If TRUE, stores the correction factor as a column named flow_marker_correction. Default is TRUE.

role

Role for generated columns.

trained

Logical indicating if the step has been trained.

skip

Logical. Should the step be skipped when baking?

id

Unique step identifier.

Value

An updated recipe with the new step added.

Details

Flow marker correction compensates for small variations in flow rate between runs. A flow marker is a small molecule (often toluene) that elutes near the total permeation volume and provides a reference point for alignment.

Correction Algorithm:

  1. Find the flow marker peak maximum within marker_range

  2. Calculate the shift: correction = observed_volume - target_volume

  3. Apply linear correction: corrected_volume = original_volume - correction

Auto-Detection:

When auto_detect = TRUE, the step uses second-derivative analysis to find the sharpest peak in the specified range, which is typically the flow marker. This is more robust than simply finding the maximum signal.

Prerequisites:

  • Should be applied before calibration and MW calculations

  • Best applied after baseline correction

Examples

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

# Apply flow marker correction with known range
rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri, location = vars(elution_volume)) |>
  step_sec_baseline() |>
  step_sec_flow_marker(
    marker_range = c(18, 20),
    target_volume = 18.5
  ) |>
  step_sec_conventional_cal(standards = ps_standards) |>
  prep()

# Auto-detect flow marker with default target (first value of range)
rec <- recipe(~., data = sec_data) |>
  step_measure_input_long(ri, location = vars(elution_volume)) |>
  step_sec_flow_marker(marker_range = c(18, 20)) |>
  prep()
} # }