In sofpn/foodvirus: A Tool For Determining Performance Criteria for Food Virology Methods

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Introduction

The EURLVerguide application is intended to aid in verification and in-house validation of quantitative PCR-based methods in food virology.

More specifically, the application is designed to analyse experiments where a dilution series of a virus has been used to artificially contaminate food samples. Typically for these experiments, a two fold dilution series is used to generate between 6-12 dilution levels (neat, 1/2, 1/4, ...) with 5-12 samples at each dilution level.

By taking dilution level and obtained concentration of each sample as input data, the application generates the following information:

• Anticipated concentration
• Information on whether the sample is detected or not
• Number of detected samples per dilution level
• Linearity
• Precision
• Limit of quantification

For more information on these performance parameters and how they are calculated, please see: ... or ...

The workflow is developed to analyse one target virus, one method, and one food type.

Installation

To install foodvirus, start R (version 4.1) and enter:

if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")
devtools::install_github("sofpn/foodvirus")

Instructions for use

Start the application

To start the application, type the following code in the R console:

foodvirus::runEURLVerguide()

The application should open in a new window.

Prepare data to upload

The input data must be formatted as a table with two columns (variables):

• dilution: describing the dilution factor of the seeding virus. A value of 1 should correspond to a "neat" dilution, a value of 0.5 to a 1/2 dilution, etc.
• obtained: describing the obtained concentration of the sample, expressed in copies/g

One row should correspond to one sample. The table should be stored in a tab-separated .txt-file, with '.' as a decimal separator, as in the example below:

Session info

This document was generated under the following conditions:

sessionInfo()

sofpn/foodvirus documentation built on Dec. 23, 2021, 3:31 a.m.