read_Xponent_csv: Read a Luminex-Xponent generated csv file

In biolabntua/moach: Multi-Omic Assay Characterization

Description

Read a Luminex-Xponent generated csv file

Usage

read_Xponent_csv(path)

Arguments

path	The path to a Luminx csv file

Details

The format details (eg comma or semicolon delimiter) are infered by the function. There is a known edge-case, for some semicolon-separated files, where some calibration information is misplaced. This is the **only** case where you should mess with the csv file, you should **not mess** with it.

Value

A list of lists with all the information from the file. At the top level there are two lists

• BatchHeader that stores all the information before the Results section as well as the CRC and

• AssayData that stores all the information in the Results section

BatchHeader stores data as key-value pairs with keys taken from the first column of the csv file and values from the rest. Values are mostly character-variables and there are few character vectors. The only exception is CALInfo with is a list of dataframes containing information about:

• Last Calibration in LastCalibration

• Classification Calibrator in ClassificationCalibratorExtended

• Reporter Calibratorin (you guessed it!) ReporterCalibrator

AssayData stores data as dataframes, except for Run data which is a list of dataframes (Audit Logs and Warning/Errors). There are 4 dataframes in AssayData:

• Exprs Expression data, ie raw data, including Medians, Counts, Net MFI, etc

• Average Averages for replicate wells

• Well Information about each well (currently only the Dilution Factor)

• Bead Information about the beads, eg BeadID

more information about the different data generated can be found here.

Author(s)

Teo Sakel

Examples

## Read a csv file for a 384 plate
path <- system.file("extdata", "test0_384.csv", package="moach")
lumcsv <- read_Xponent_csv(path)

biolabntua/moach documentation built on May 12, 2019, 9:24 p.m.