read_luminex_data: Read Luminex Data

In SerolyzeR: Reading, Quality Control and Preprocessing of MBA (Multiplex Bead Assay) Data

Read Luminex Data

Description

Reads a Luminex plate file and returns a Plate object containing the extracted data. Optionally, a layout file can be provided to specify the arrangement of samples on the plate.

The function supports two Luminex data formats:

• xPONENT: Used by older Luminex machines.

• INTELLIFLEX: Used by newer Luminex devices.

Workflow

1. Validate input parameters, ensuring the specified format is supported.

2. Read the plate file using the appropriate parser:

   • xPONENT files are read using read_xponent_format().

   • INTELLIFLEX files are read using read_intelliflex_format().

3. Post-process the extracted data:

   • Validate required data columns (Median, Count).

   • Extract sample locations and analyte names.

   • Parse the date and time of the experiment.

File Structure

• Plate File (plate_filepath): A CSV file containing Luminex fluorescence intensity data.

• Layout File (layout_filepath) (optional): An Excel or CSV file containing the plate layout.

  • The layout file should contain a table with 8 rows and 12 columns, where each cell corresponds to a well location.

  • The values in the table represent the sample names for each well.

Sample types detection

The read_luminex_data method automatically detects the sample types based on the sample names, unless provided the sample_types parameter. The sample types are detected used the translate_sample_names_to_sample_types method. In the documentation of this method, which can be accessed with command ?translate_sample_names_to_sample_types, you can find the detailed description of the sample types detection.

Usage

read_luminex_data(
  plate_filepath,
  layout_filepath = NULL,
  format = "xPONENT",
  plate_file_separator = ",",
  plate_file_encoding = "UTF-8",
  use_layout_sample_names = TRUE,
  use_layout_types = TRUE,
  use_layout_dilutions = TRUE,
  default_data_type = "Median",
  sample_types = NULL,
  dilutions = NULL,
  verbose = TRUE
)

Arguments

plate_filepath	(character(1)) Path to the Luminex plate file.
layout_filepath	(character(1), optional) Path to the Luminex layout file.
format	(character(1), default = 'xPONENT') The format of the Luminex data file. Supported formats: 'xPONENT', 'INTELLIFLEX'.
plate_file_separator	(character(1), default = ',') The delimiter used in the plate file (CSV format). Used only for the xPONENT format.
plate_file_encoding	(character(1), default = 'UTF-8') The encoding used for reading the plate file. Used only for the xPONENT format.
use_layout_sample_names	(logical(1), default = TRUE) Whether to use sample names from the layout file.
use_layout_types	(logical(1), default = TRUE) Whether to use sample types from the layout file (requires a layout file).
use_layout_dilutions	(logical(1), default = TRUE) Whether to use dilution values from the layout file (requires a layout file).
default_data_type	(character(1), default = 'Median') The default data type used if none is explicitly provided.
sample_types	(character(), optional) A vector of sample types to override extracted values.
dilutions	(numeric(), optional) A vector of dilutions to override extracted values.
verbose	(logical(1), default = TRUE) Whether to print additional information and warnings.

Value

A Plate object containing the parsed Luminex data.

Examples

# Read a Luminex plate file with an associated layout file
plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "SerolyzeR")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "SerolyzeR")
plate <- read_luminex_data(plate_file, layout_file)

# Read a Luminex plate file without a layout file
plate_file <- system.file("extdata", "CovidOISExPONTENT_CO.csv", package = "SerolyzeR")
plate <- read_luminex_data(plate_file, verbose = FALSE)

SerolyzeR documentation built on April 12, 2025, 2:11 a.m.