read.multiplex: Load raw data from multiplex (x-MAP technology) run file.

In immunoassay: Functions for working with immunoassay data.

Description

This fuction reads a multiplex run .csv file from a given folder and extracts raw data from it (MFI, counts, results and fit information, if available). It returns an object of class ima which is a specifically formatted data.frame with immunoassay run parameters stored as attributes.

Usage

 read.multiplex(path, file, analytes = "all") 

Arguments

path	Character. The path to the data file.
file	Character. Filename of the file to load. Does not need to contain ".csv" extension - it will be added automatically.
analytes	Either character 'analytes="all"' to load all available analytes, or a numeric vector, to select from the analytes available in the data.

Details

This function reads the raw data from multiplex run files: MFIs, COUNTs results, run information. It can also load nominal concentrations of Standards and QCs along with fit information, if available (currently "xPONENT" files only).

It then creates a specifically formatted data frame with many run parameters stored as attributes. It can currently recognize two ".csv" file formats - the "Luminex IS" and "xPONENT" output. If your file doesn't load properly, please email it to the author for evaluation.

Value

This function returns a structure of class ima composed of the following elements:

data	A data.frame with the actual data.
file	File name.
Assay	Character vector with the assay infromation (platform, S/N and session name).
Lot	Character vector with reagent Lot # and a number of samples.
Analytes	Character vector of analyte names.
Units	Character vector of analyte units.
calibrators	A data.frame with nominal concentrations of kit calibrators and QCs.
Date	The date the run was processed.
Operator	Name of the analyst that processed the run.
Background	Numeric vector of background values for all analytes.

Note

Currently the function can process data files from "Luminex IS" and "xPONENT" software platforms. Tested on run files with few analytes only. Please email problem files to the author.

Author(s)

Michal J. Figurski, PhD [e-mail]

See Also

sigfit and read.kits.

Examples

## Not run: 
    run = read.multiplex("your-path-here","filename.csv")
    run
    plot(run)
    summary(run, analyte=1)

## End(Not run)

immunoassay documentation built on May 2, 2019, 4:45 p.m.