RT Journal Article
SR Electronic
T1 GCalignR: An R package for aligning Gas-Chromatography data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 110494
DO 10.1101/110494
A1 Meinolf Ottensmann
A1 Martin A. Stoffel
A1 Hazel J. Nichols
A1 Joseph I. Hoffman
YR 2017
UL http://biorxiv.org/content/early/2017/09/14/110494.abstract
AB Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, gas chromatography (GC) in combination with either mass spectrometry (MS) or flame ionisation detection (FID) are commonly used to characterise complex chemical samples. Both GC-FID and GC-MS generate chromatograms comprising peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present GCalignR, a user-friendly R package for aligning GC-FID data based on retention times. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments, and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that GCalignR performed equally well or better than other available software. We hope that GCalignR will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields.