Read Luminex Data — read_luminex

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.

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)
#> Reading Luminex data from: /home/runner/work/_temp/Library/PvSTATEM/extdata/CovidOISExPONTENT.csv
#> using format xPONENT
#> 
#> New plate object has been created with name: CovidOISExPONTENT!
#> 

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