chromatographR-package: chromatographR

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

chromatographR

Description

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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btv299")}) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/S0021-9673(01)00594-5")}). More details on package usage and a suggested workflow can be found in the vignette.

Data

• preprocess: A list of four goldenrod root chromatograms.

• Sa_pr: Preprocessed goldenrod root chromatograms.

• Sa_warp: Preprocessed and aligned goldenrod root chromatograms.

• pk_tab: Peak table from aligned goldenrod root chromatograms.

• Sa: A list of four goldenrod root chromatograms.

• Sa_pr: Preprocessed goldenrod root chromatograms.

• Sa_warp: Preprocessed and aligned goldenrod root chromatograms.

• pk_tab: Peak table from aligned goldenrod root chromatograms.

Author(s)

Ethan Bass

See Also

Useful links:

• https://ethanbass.github.io/chromatographR/

• https://github.com/ethanbass/chromatographR/

• Report bugs at https://github.com/ethanbass/chromatographR/issues/

ethanbass/chromatographR documentation built on April 17, 2025, 10:55 a.m.