RDML

RDML: R Package for RDML-Based qPCR Data Management and Transformation

RDML imports, parses, and manipulates quantitative PCR (qPCR) data stored in Real-time PCR Data Markup Language (RDML) format within the R environment, enabling standardized data extraction, transformation, and file generation.

Key Features:

• RDML Standard Compatibility: Supports RDML format versions up to 1.2 for standardized qPCR data exchange.
• Data Import and Transformation: Imports RDML files into R and converts data into formats compatible with the R packages qpcR and chipPCR.
• Sample Metadata Extraction: Extracts target identifiers, concentrations, and associated sample metadata directly from RDML files.
• Run Summarization and File Generation: Generates structured summaries of qPCR runs and creates new RDML files from user-defined data.
• Dendrogram Visualization: Produces dendrograms representing the hierarchical structure of RDML objects for structural interpretation.

Scientific Applications:

• qPCR Data Analysis and Standardization: Supports standardized management, transformation, and integration of qPCR datasets for reproducible analysis and interoperability with R-based analytical workflows.

Methodology:

RDML imports qPCR data encoded in RDML format into R, parses hierarchical RDML structures, extracts experimental and sample-level metadata, transforms data into analysis-ready objects compatible with qpcR and chipPCR, generates structured run summaries, and constructs RDML-compliant output files.