A collection of functions for top-down exploratory data analysis of spectral data including nuclear magnetic resonance (NMR), infrared (IR), Raman, X-ray fluorescence (XRF) and other similar types of spectroscopy. Includes functions for plotting and inspecting spectra, peak alignment, hierarchical cluster analysis (HCA), principal components analysis (PCA) and model-based clustering. Robust methods appropriate for this type of high-dimensional data are available. ChemoSpec is designed for structured experiments, such as metabolomics investigations, where the samples fall into treatment and control groups. Graphical output is formatted consistently for publication quality plots. ChemoSpec is intended to be very user friendly and to help you get usable results quickly. A vignette covering typical operations is available.
files2SpectraObjectcan now accept any arguments to
read.tablevia the ... mechanism. Arguments are sanitized more robustly. However, it is possible to pass arguments that may not be of real utility. For instance
na.stringscan be specified, but any
NAin the data imported will trigger warnings and errors.
files2SpectraObjectcan now accept optional arguments
recursiveto allow reading through a directory substructure. In addition, a progress bar is now displayed unless
debug = TRUE. Both features suggested by Reinhard Kerschner along with preliminary code (thanks!).
.groupNcolor(the problem seems to have been present from the very beginning). Reported by Reinhard Kerschner (many thanks!). Note
.groupNcolornow resides in
ChemoSpecUtils. Reported here for convenience.
tryCatch()to more gracefully fail and offer suggestions to user.
news(package = "ChemoSpec").