read_luminex_data {SerolyzeR} | R Documentation |
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
Validate input parameters, ensuring the specified format is supported.
Read the plate file using the appropriate parser:
xPONENT files are read using
read_xponent_format()
.INTELLIFLEX files are read using
read_intelliflex_format()
.
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 |
( |
layout_filepath |
( |
format |
(
|
plate_file_separator |
(
|
plate_file_encoding |
(
|
use_layout_sample_names |
(
|
use_layout_types |
(
|
use_layout_dilutions |
(
|
default_data_type |
(
|
sample_types |
( |
dilutions |
( |
verbose |
(
|
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)