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Median Fluorescent Intensity (MFI) to Relative Antibody Units (RAU) conversion

Source: R/MFItoRAU.R
MFItoRAU.Rd

This function fits a 5-parameter logistic standard curve to the dilutions of the positive controls for each protein and converts the MFI values into relative antibody units (RAU) written by Connie Li Wai Suen.

Usage

MFItoRAU(sero_data, plate_list, qc_results, std_point = 10, project = NULL)

Arguments

sero_data

Output from `readSeroData()`.

plate_list

Output from `readPlateLayout()`.

qc_results

Output from `runQC()`.

std_point

Standard Point Curve: 5 = 5-point curve, 10 = 10-point curve, "PvLDH" for LDH specific curve. Default = 10. Value is an integer.

project

Default = NULL. Only write "pkpfpv" if using Pk/Pf/Pv pipeline.

Value

A list of three data frames: 1. Data frame with MFI data, converted RAU data and matched SampleID's. 2. Plot information for `plotModel` function 3. Data frame of RAU data for random forest classification use.

Author

Dionne Argyropoulos, Connie Li Wai Suen

Examples

# \donttest{

# Step 0: Load example raw data
your_raw_data <- c(
  system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR"),
  system.file("extdata", "example_MAGPIX_plate2.csv", package = "SeroTrackR")
)
your_plate_layout <- system.file(
  "extdata",
  "example_platelayout_1.xlsx",
  package = "SeroTrackR"
)

# Step 1: Read serology data and plate layout
sero_data  <- readSeroData(your_raw_data,"magpix")
#> PASS: File example_magpix_plate1.csv successfully validated.
#> PASS: File example_magpix_plate2.csv successfully validated.
plate_list <- readPlateLayout(your_plate_layout, sero_data)
#> Plate layouts correctly identified!

# Step 2: Process counts and perform quality control
qc_results  <- runQC(sero_data, plate_list)

# Step 3: Convert MFI to RAU
mfi_to_rau <- MFItoRAU(
  sero_data = sero_data,
  plate_list = plate_list,
  qc_results = qc_results
)

# }