The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.