moritzlindner / ephysdata

Data Structures for Electropysiological Recordings

EPhysData R Package

Introduction

The EPhysData package provides a set of tools and classes for working with electrophysiological data in R. This package is designed to streamline the process of importing and preprocessing electrophysiological data, making it easier for researchers and analysts to work with complex datasets.

There are two classes for storing the data. The EPhysData class stores data from a single recording (possibly with repeated measurements). It is usually generated from imported raw data using newEPhysSet(). Information on how to filter or average the data contained in this class can be stored in it, but the data is left unchanged. The EPhysSet class contains a collection of associated EPhysData classes (e.g. data from different channels recorded in parallel or in response to increasing stimulus intensities). Each EPhysData stored is associated with metadata describing the nature of the particular recodring. This class can be subsetted, extended or modified in other ways.

Installation

You can install the development version of EPhysData like so:

if (!requireNamespace("remotes", quietly = TRUE)){
  install.packages("remotes")
}
remotes::install_github("moritzlindner/EPhysData")

Note that EPhysData recommends the github-deposited R Package EPhysMethods. Installation usually works automatically. Updating, however may fail. If this is the case, update manually using the following line of code:

remotes::install_github("moritzlindner/EPhysMethods")

Example

This is a basic example which shows you how to solve a common problem:

# Load the EPhysData package
library(EPhysData)

# Create an example EPhysData object
data <- makeExampleEPhysData()

# Get data
GetData(data, Raw = T)

# Get time trace data
TimeTrace(data)

# Set Averaging and function for the data
FilterFunction(data)<-function(x){x/max(x)}
GetData(data, Raw = F)
#> Warning in GetData(data, Raw = F): Averaging function function (x) { x} returns more than a single value per time point. Has a valid function been
#> set? Try e.g.: AverageFunction(X)<-mean
AverageFunction(data)<-function(x){mean(x)}
GetData(data, Raw = F)

# Create an EPhysSet object
ephysSet <-
  newEPhysSet(
    Data = list(
      makeExampleEPhysData(),
      makeExampleEPhysData(),
      makeExampleEPhysData(),
      makeExampleEPhysData()
    ),
    Metadata = data.frame(StepID = c("A1", "A2", "A3", "A4"))
  )
ephysSet

Documentation

Please see the EPhysData-package-page accessible via the package’s help index for a systematic description of the functions and methods included into the package.