GCalignR

GCalignR aligns gas chromatography–flame ionization detection (GC-FID) chromatographic peaks across biological samples to standardize retention-time-based chemical profiles for ecological and evolutionary analyses.

Key Features:

• Retention time-based alignment: Aligns chromatographic peaks by retention times to match homologous substances across samples such as skin swabs while accounting for inter-sample variability.
• Parameter tuning and error estimation: Exposes alignment parameters and computes alignment error rates to evaluate and optimize settings across datasets.
• Visualization functions: Provides visualization routines to inspect alignment quality and assess peak matching across chromatograms.
• R integration: Implements functions within the R environment to integrate peak alignment outputs into R-based analysis workflows and downstream multivariate analyses.
• Empirical validation: Demonstrated on empirical GC-FID data from Antarctic fur seals, reporting low error rates across a range of parameter settings and competitive performance versus other alignment software.

Scientific Applications:

• Animal chemical communication: Enables comparative chemical profiling for studies of mate choice, kin recognition, and other chemically mediated behaviors.
• Eco-evolutionary analyses: Supports comparison of chemical profiles across sexes, age classes, and reproductive stages to investigate eco-evolutionary patterns.
• Downstream statistical analysis: Produces standardized peak matrices suitable for multivariate statistical analyses of complex chemical datasets.

Methodology:

Aligns peaks by retention time while accounting for experimental noise, allows user-defined alignment parameters, and calculates alignment error rates for optimization.