Convert continuous-wave fNIRS intensity to optical density

Optical density is calculated with the natural-log convention -log(I / I0). The reference intensity and any replacement of non-positive cells are explicit and recorded in provenance.

Usage

intensityToOD(
  x,
  assay_name = NULL,
  baseline = c("mean", "median"),
  baseline_interval = NULL,
  reference = NULL,
  nonpositive = c("error", "replace"),
  replacement = NULL,
  output_assay = "OD"
)

Arguments

x: A governed continuous-wave PhysioExperiment.
assay_name: Exact input assay name. NULL is allowed only when one eligible intensity assay exists.
baseline: Exactly "mean" or "median".
baseline_interval: Optional closed interval in seconds.
reference: Optional positive scalar or vector with one value per measurement.
nonpositive: Exactly "error" or "replace".
replacement: Explicit positive scalar used only with nonpositive = "replace".
output_assay: Exact name for the new optical-density assay.

Value

x with a unitless optical-density assay appended.

Examples

pe <- PhysioNIRS:::.nirs_demo_object()
od <- intensityToOD(pe)
SummarizedExperiment::assayNames(od)
#> [1] "raw" "OD"