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excelDataGuide

excelDataGuide simplifies reading data from Excel data reporting templates (DRT’s) into R.

A data reporting template is an Excel file for standardized reporting and processing of experimental data. The template encourages or forces users to provide data in a structured manner that minimizes errors and misinterpretation.

The package provides a simple interface to read data from Excel files and convert them into R objects. We assume that data is organized in three types of data structures; key-value pairs, tabular data and microplateplate-formatted data. The locations of these data structures in the Excel template are provided by a data guide. A data guide is a YAML file designed for a specific data reporting template.

Installation

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

# install.packages("pak")
pak::pak("SystemsBioinformatics/excelDataGuide")

Example

The basic usage of the package only requires one command with two file paths: the path to the Excel data file and the path to the data guide file. Here is an example:

library(excelDataGuide)
datafile <- system.file("extdata", "example_data.xlsx", package = "excelDataGuide")
guidefile <- system.file("extdata", "example_guide.yml", package = "excelDataGuide")
data <- read_data(datafile, guidefile)

The output of the read_data() function is a list object containing the data in a structured manner. The structure is determined for a large part by the design of the data guide.

Three types of data structure

We assume that data structures can be either of three types:

  • Key-value pairs, where a value is the content of a single cell or of a number of adjacent cells. They correspond to and are stored in R as atomic vectors with a single or multiple values
  • Tables, where data is organized in tabular format with variables in columns. This corresponds directly to the data.frame in R.
  • Microplate data, where values are stored in the same rectangular format as they are read from microplates.