Chromatographic Data Analysis Toolset
Details
Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. doi:10.1093/bioinformatics/btv299 ). Alignment of chromatograms is available using parametric time warping (PTW) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. doi:10.1093/bioinformatics/btv299 ) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. doi:10.18637/jss.v047.i08 ). Peak-finding relies on the algorithm suggested by Tom O'Haver in his Pragmatic Introduction to Signal Processing. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. doi:10.1016/S0021-9673(01)00594-5 ). More details on package usage and a suggested workflow can be found in the vignette.
Analysis functions
read_chroms(): Import chromatograms from a variety of vendor formats.preprocess(): Preprocess chromatographic matrices.correct_rt(): Align chromatograms.get_peaks(): Find and integrate peaks.get_peaktable(): Assemble peak table.attach_metadata(): Attach metadata to peak table.attach_ref_spectra(): Attach reference spectra to peak table.normalize_data(): Normalizepeaktableorchrom_list.
Visualization functions
boxplot.peak_table(): Create boxplot from peaktable object.plot_chroms(): Plot chromatograms as traces.plot_chroms_heatmap(): Plot chromatograms as heatmap.plot_spectrum(): Plot spectrum and/or trace of specified peak.plot_all_spectra(): Plot all spectra for specified peak.mirror_plot(): Plot chromatograms as mirror plot.scan_chrom(): Plot spectrum at wavelength specified by clicking on a chromatogram.plot.peak_list(): Plot fitted peaks over chromatographic trace.plot.peak_table(): Plot the trace and/or spectrum of a specified peak from the peak table.plot.ptw_list(): Plot PTW alignment object.
Utility functions
combine_peaks(): Combine duplicate peaks in peak table based on retention time and spectral similarity.merge_peaks(): Merge split peaks into a single column of a peak table.get_times(): Return retention times from a peak table or a list of chromatograms.get_lambdas(): Return wavelengths from a peak table or a list of chromatograms.reshape_chroms(): Reshape a list of chromatograms to long format.reshape_peaktable(): Reshape apeak_tableobject to long format.write_peaktable(): Export peak table incsvorxlsxformat.