rconf is a minimal and lightweight configurationtool for R that supports reading basic YAML configuration files withoutany additional package dependencies. It is designed for quick prototypesand lightweight projects, such as proteomics data analysispipelines.
install.packages("rconf")Place your YAML configuration file in a convenient location. Forexample, the package includes a sample configuration file in theinst/extdata/ directory. You can load it as follows:
# Load the rconf packagelibrary(rconf)# Load configuration from the sample file in extdatacfg<-get_config(system.file("extdata","config.yml",package ="rconf"))# Access configuration settingsraw_dir<- cfg$raw_data_dirprocessed_dir<- cfg$processed_data_dirmetadata_file<- cfg$sample_metadatanormalization<- cfg$normalization_methodfdr_cutoff<- cfg$protein_fdr# Print valuesprint(raw_dir)print(processed_dir)print(metadata_file)print(normalization)print(fdr_cutoff)The sample YAML configuration file included with rconf (located atinst/extdata/config.yml) is designed for a proteomics data analysisproject. It might look like this:
default: # Data directories and filesraw_data_dir:"/data/proteomics/raw"processed_data_dir:"/data/proteomics/processed"sample_metadata:"/data/proteomics/metadata/samples.csv" # Analysis parametersnormalization_method:"median"quantification:"LFQ"protein_fdr:0.01 # Statistical analysis optionsdifferential_expression:truep_value_cutoff:0.05 # Plotting optionsplot:output_dir:"results/plots"format:"png"dpi:300The package includes unit tests (using testthat) to ensure that YAMLconfigurations are parsed correctly. See the tests in thetests/testthat/ directory for examples.
GPL-3