SerolyzeR (version 1.1.0)

read_luminex_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
)

Value

A Plate object containing the parsed Luminex data.

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.

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)