process_file {SerolyzeR} | R Documentation |
Process a File to Generate Normalised Data and Reports
Description
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
Read the plate file and layout file.
Process the plate data using the specified normalisation types (
MFI
,RAU
,nMFI
).Save the processed data to CSV files in the specified
output_dir
. The files are named as{plate_name}_{normalisation_type}.csv
.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 |
( |
layout_filepath |
( |
output_dir |
(
|
format |
(
|
generate_report |
(
|
process_plate |
(
|
normalisation_types |
(
|
blank_adjustment |
(
|
verbose |
(
|
... |
Additional arguments passed to |
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)
# Example 2: Process the plate for only RAU normalisation
process_file(plate_file, layout_file, output_dir = example_dir, normalisation_types = c("RAU"))
# Example 3: Process the plate and generate a quality control report
process_file(plate_file, layout_file, output_dir = example_dir, generate_report = TRUE)