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Read Luminex Data

Source: R/parser.R
read_luminex_data.Rd

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)
#> 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")
# To suppress warnings and additional information use verbose = FALSE
plate <- read_luminex_data(plate_file, layout_file, verbose = FALSE)