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Process a File to Generate Normalised Data and Reports

Source: R/process-file.R
process_file.Rd

This function reads a Luminex plate file by calling read_luminex_data() and then processes it by calling process_plate(). It optionally generates also a quality control report using generate_plate_report(). It reads the specified plate file, processes the plate object using all specified normalisation types (including raw MFI values), and saves the results. If generate_report = TRUE, a quality control report is also generated.

Workflow

  1. Read the plate file and layout file.

  2. Process the plate data using the specified normalisation types (MFI, RAU, nMFI).

  3. Save the processed data to CSV files in the specified output_dir. The files are named as {plate_name}_{normalisation_type}.csv.

  4. Optionally, generate a quality control report. The report is saved as an HTML file in the output_dir, under the name {plate_name}_report.html.

Usage

process_file(
  plate_filepath,
  layout_filepath,
  output_dir = "normalised_data",
  format = "xPONENT",
  generate_report = FALSE,
  process_plate = TRUE,
  normalisation_types = c("MFI", "RAU", "nMFI"),
  blank_adjustment = FALSE,
  verbose = TRUE,
  ...
)

Arguments

plate_filepath

(character(1)) Path to the Luminex plate file.

layout_filepath

(character(1)) Path to the corresponding layout file.

output_dir

(character(1), default = 'normalised_data')

  • Directory where the output files will be saved.

  • If it does not exist, it will be created.

format

(character(1), default = 'xPONENT')

  • Format of the Luminex data.

  • Available options: 'xPONENT', 'INTELLIFLEX'.

generate_report

(logical(1), default = FALSE)

process_plate

(logical(1), default = TRUE)

  • If TRUE, processes the plate data using process_plate().

  • If FALSE, only reads the plate file and returns the plate object without processing.

normalisation_types

(character(), default = c("MFI", "RAU", "nMFI"))

  • List of normalisation types to apply.

  • Supported values: c("MFI", "RAU", "nMFI").

blank_adjustment

(logical(1), default = FALSE)

  • If TRUE, performs blank adjustment before processing.

verbose

(logical(1), default = TRUE)

  • If TRUE, prints additional information during execution.

...

Additional arguments passed to read_luminex_data() and generate_plate_report().

Value

A Plate object containing the processed data.

Examples

# Example 1: Process a plate file with default settings (all normalisation types)
plate_file <- system.file("extdata", "CovidOISExPONTENT_CO_reduced.csv", package = "SerolyzeR")
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "SerolyzeR")
example_dir <- tempdir(check = TRUE)
process_file(plate_file, layout_file, output_dir = example_dir)
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/CovidOISExPONTENT_CO_reduced.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: CovidOISExPONTENT_CO_reduced!
#> 
#> Processing plate 'CovidOISExPONTENT_CO_reduced'
#> Extracting the raw MFI to the output dataframe
#> Saving the computed MFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_MFI.csv'
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_RAU.csv'
#> Computing nMFI values for each analyte
#> Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_nMFI.csv'
#> Plate with 49 samples and 2 analytes

# Example 2: Process the plate for only RAU normalisation
process_file(plate_file, layout_file, output_dir = example_dir, normalisation_types = c("RAU"))
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/CovidOISExPONTENT_CO_reduced.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: CovidOISExPONTENT_CO_reduced!
#> 
#> Processing plate 'CovidOISExPONTENT_CO_reduced'
#> Warning: The specified file /tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_RAU.csv already exists. Overwriting it.
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_RAU.csv'
#> Plate with 49 samples and 2 analytes

# Example 3: Process the plate and generate a quality control report
process_file(plate_file, layout_file, output_dir = example_dir, generate_report = TRUE)
#> Reading Luminex data from: /home/runner/work/_temp/Library/SerolyzeR/extdata/CovidOISExPONTENT_CO_reduced.csv
#> using format xPONENT
#> Could not parse datetime string using default datetime format. Trying other possibilies.
#> Successfully parsed datetime string using order: mdY IM p
#> 
#> New plate object has been created with name: CovidOISExPONTENT_CO_reduced!
#> 
#> Processing plate 'CovidOISExPONTENT_CO_reduced'
#> Warning: The specified file /tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_MFI.csv already exists. Overwriting it.
#> Extracting the raw MFI to the output dataframe
#> Saving the computed MFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_MFI.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_RAU.csv already exists. Overwriting it.
#> Fitting the models and predicting RAU for each analyte
#> Saving the computed RAU values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_RAU.csv'
#> Warning: The specified file /tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_nMFI.csv already exists. Overwriting it.
#> Computing nMFI values for each analyte
#> Saving the computed nMFI values to a CSV file located in: '/tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_nMFI.csv'
#> Generating report...This will take approximately 30 seconds.
#> Warning: The specified file /tmp/Rtmpl5e8H2/CovidOISExPONTENT_CO_reduced_report.html already exists. Overwriting it.
#> Report successfully generated, saving to: /tmp/Rtmpl5e8H2
#> Plate with 49 samples and 2 analytes