rconf

rconf is a minimal and lightweight configuration tool for R that supports reading basic YAML configuration files without any additional package dependencies. It is designed for quick prototypes and lightweight projects, such as proteomics data analysis pipelines.

Features

Parse basic YAML configuration files
No external dependencies
Easy-to-use API for loading and accessing configuration settings

Installation

install.packages("rconf")

Usage

Place your YAML configuration file in a convenient location. For example, the package includes a sample configuration file in the inst/extdata/ directory. You can load it as follows:

# Load the rconf package
library(rconf)

# Load configuration from the sample file in extdata
cfg <- get_config(system.file("extdata", "config.yml", package = "rconf"))

# Access configuration settings
raw_dir         <- cfg$raw_data_dir
processed_dir   <- cfg$processed_data_dir
metadata_file   <- cfg$sample_metadata
normalization   <- cfg$normalization_method
fdr_cutoff      <- cfg$protein_fdr

# Print values
print(raw_dir)
print(processed_dir)
print(metadata_file)
print(normalization)
print(fdr_cutoff)

Sample Configuration File

The sample YAML configuration file included with rconf (located at inst/extdata/config.yml) is designed for a proteomics data analysis project. It might look like this:

default:
  # Data directories and files
  raw_data_dir: "/data/proteomics/raw"
  processed_data_dir: "/data/proteomics/processed"
  sample_metadata: "/data/proteomics/metadata/samples.csv"

  # Analysis parameters
  normalization_method: "median"
  quantification: "LFQ"
  protein_fdr: 0.01

  # Statistical analysis options
  differential_expression: true
  p_value_cutoff: 0.05

  # Plotting options
  plot:
    output_dir: "results/plots"
    format: "png"
    dpi: 300

Unit Testing

The package includes unit tests (using testthat) to ensure that YAML configurations are parsed correctly. See the tests in the tests/testthat/ directory for examples.

License

GPL-3