read_luminex_data: Read Luminex Data

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

Read Luminex Data

Description

Reads a file containing Luminex data and returns a Plate object. If provided, can also read a layout file, which usually contains information about the sample names, sample types or its dilutions.

The function is capable of reading data in two different formats:

• xPONENT

• INTELLIFLEX which are produced by two different Luminex machines.

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	Path to the Luminex plate file
layout_filepath	Path to the Luminex layout file
format	The format of the Luminex data. Select from: xPONENT, INTELLIFLEX
plate_file_separator	The separator used in the plate file
plate_file_encoding	The encoding used in the plate file
use_layout_sample_names	Whether to use names from the layout file in extracting sample names.
use_layout_types	Whether to use names from the layout file in extracting sample types. Works only when layout file is provided
use_layout_dilutions	Whether to use dilutions from the layout file in extracting dilutions. Works only when layout file is provided
default_data_type	The default data type to use if none is specified
sample_types	a vector of sample types to use instead of the extracted ones
dilutions	a vector of dilutions to use instead of the extracted ones
verbose	Whether to print additional information and warnings. TRUE by default

Value

Plate file containing the Luminex data

Examples

plate_file <- system.file("extdata", "CovidOISExPONTENT.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_layout.csv", package = "PvSTATEM")
plate <- read_luminex_data(plate_file, layout_file)

plate_file <- system.file("extdata", "CovidOISExPONTENT_CO.csv", package = "PvSTATEM")
layout_file <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx", package = "PvSTATEM")
# To suppress warnings and additional information use verbose = FALSE
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)

PvSTATEM documentation built on April 4, 2025, 4:34 a.m.