Run Pk/Pf/Pv Data Analysis Pipeline from Start to End

Usage

runPlasmoPipeline(
  raw_data,
  platform = "magpix",
  plate_layout,
  panel = "panel1",
  std_point,
  experiment_name = "experiment1",
  classify = "Yes",
  algorithm_type = "antibody_model",
  sens_spec = "balanced"
)

Arguments

raw_data: String with the raw data path.
platform: "magpix" or "bioplex". Default: "Bioplex"
plate_layout: An ".xlsx" file with sheets labelled plate1, plate2... etc.
panel: Panel of Pk/Pf/Pv antigens. Default = "panel1" or user provided csv of Antigens and Species.
std_point: Standard Point Curve: 5 = 5-point curve, 10 = 10-point curve. Value is an integer.
experiment_name: User-input experiment name. Default: "experiment1".
classify: "Yes" or "No" depending on whether you would like classification or not. Default = "Yes".
algorithm_type: User-selected algorithm choice: - "antibody_model" (PvSeroTaT model; default), or - "antibody_model_excLF016" (PvSeroTaT excluding LF016).
sens_spec: User-selected Sensitivity/Specificity threshold: - "balanced" (default), - "85% sensitivity", - "90% sensitivity", - "95% sensitivity", - "85% specificity", - "90% specificity". - "95% specificity".

Value

A data frame containing the MFI and RAU Dilution values for each sample, QC plots for standard curve, bead counts and blanks.

Author

Dionne Argyropoulos

Examples

# \donttest{

# Helper to avoid repetition in examples
run_example_std <- function(std_point) {
  # Load raw data for given standard curve
  your_raw_data <- c(
    system.file("extdata",
                paste0("example_MAGPIX_pk_", std_point, "std_plate1.csv"),
                package = "SeroTrackR"),
    system.file("extdata",
                paste0("example_MAGPIX_pk_", std_point, "std_plate2.csv"),
                package = "SeroTrackR")
  )

  layout_file <- system.file(
    "extdata",
    paste0("example_platelayout_pk_", std_point, "std.xlsx"),
    package = "SeroTrackR"
  )

  # Run pipeline
  runPlasmoPipeline(
    raw_data = your_raw_data,
    platform = "magpix",
    plate_layout = layout_file,
    panel = "panel1",
    std_point = std_point,
    experiment_name = paste0(std_point, "-point standard curve")
  )
}

# ---- 5-point standard curve ----
results_5std <- run_example_std(5)
#> PASS: File example_magpix_pk_5std_plate1.csv successfully validated.
#> PASS: File example_magpix_pk_5std_plate2.csv successfully validated.
#> Plate layouts correctly identified!
#> QC Processes completed.
#> QC Plotting completed.
#> MFI to RAU conversion completed.
#> Pv classification completed.

# ---- 10-point standard curve ----
results_10std <- run_example_std(10)
#> PASS: File example_magpix_pk_10std_plate1.csv successfully validated.
#> PASS: File example_magpix_pk_10std_plate2.csv successfully validated.
#> Plate layouts correctly identified!
#> QC Processes completed.
#> QC Plotting completed.
#> MFI to RAU conversion completed.
#> Pv classification completed.

# }