Apply preprocessing pipeline

Applies a preprocessing pipeline to a PhysioExperiment object.

Usage

applyPipeline(pe, pipeline, verbose = FALSE)

Arguments

pe

A PhysioExperiment object.

pipeline

A pipeline object created with createPipeline().

verbose

Logical. If TRUE, prints progress messages.

Value

PhysioExperiment with all pipeline steps applied.

References

Oppenheim AV, Willsky AS, Nawab SH (1997). "Signals and Systems." 2nd ed. Prentice Hall.

See also

createPipeline() for defining the pipeline steps, butterworthFilter() and resample() for common preprocessing operations used within pipelines.

Examples

pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(1000), nrow = 100, ncol = 10)),
  colData = S4Vectors::DataFrame(label = paste0("Ch", 1:10)),
  samplingRate = 256
)
pipeline <- createPipeline(
  detrend = list(fn = "detrendSignals", method = "linear")
)
pe_processed <- applyPipeline(pe, pipeline)