MEAanalysis

The goal of MEAanalysis is to analyse files from the MEA machine.

Installation

You can install the development version of MEAanalysis from GitHub with:

# install.packages("devtools")
devtools::install_github("ankemt/MEAanalysis")

Getting started

This package is under active development. Currently, it can be used to create a tidy data object that aggregates data from baseline and exposure neural metrics output files.

Step 1: create an inputfile with the experimental design

This can be done with the following function:

MEAanalysis::exp_design()

This call prompts a few questions: first, the date of the experiment and the experiment ID. For example, the experiment TestExperiment done on October 3rd 2020:

What is the date of the experiment? (YYYYMMDD) 20201003
What is the experiment ID? TestExperiment

Then, you can add well ranges for the different experimental conditions. For example, here is how to add a range of wells for the control:

What is the experimental condition? control
In what direction ('LR' for left-to-right or 'TB' for top-to-bottom) is the sequence of wells? TB
What is the first well in this category? (e.g.: A1) A1
What is the last well in this category? (e.g.: F8) B2
Do you want to add another group? (y/n) n

This generates the file design.txt saved in the current working directory, with the following content:

Date: 20201003
ExperimentID: TestExperiment
Total_wells: 48
Groups:
control: A1 B1 C1 D1 E1 F1 A2 B2

This file can of course also be generated and edited by hand. At the moment the well range functionality only works for 48 well plates. If your input uses a different plate format the design file should be edited by hand.

Step 2: Calculate the experiment's treatment ratio

For this function, three input files are required:

The neural metrics for the baseline (a .csv file)
The neural metrics for the exposure (a .csv file)
The design file created under step 1.

Calculate the treatment ratio as follows:

data <- MEAanalysis::treatment_ratio(
          exposurepath = "path/to/exposurefile.csv",
          baselinepath = "path/to/baselinefile.csv",
          designpath = "path/to/design.txt")

The object created here contains the raw values from both input files (Baseline_value and Exposure_value) for all wells (included in the design.txt file) and parameters, as well as the Treatment_ratio, a calculation of exposure/baseline.

Trial use & feedback

We are very happy with your feedback! Please let us know your experience with this package by creating an issue, or by emailing Anke Tukker directly at atukker@purdue.edu.

ankemt / MEAanalysis