Chromatographic Data Analysis Toolset

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. . Alignment of chromatograms is available using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. ) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. ). Peak-finding uses the algorithm by Tom O'Haver < http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. ). See the vignette for more details and suggested workflow.

chromatographR

Overview

chromatographR is a package for the reproducible analysis of HPLC-DAD chromatographic data in R. It can also be used to analyze other "simple" chromatographic data like GC-FID, HPLC-UV, or HPLC-FD.

Installation

chromatographR can now be installed from CRAN:

install.packages("chromatographR")

You can also install the latest development version of chromatographR from GitHub using the devtools package:

install.packages("devtools")
devtools::install_github("https://github.com/ethanbass/chromatographR/")

To build the vignette, include the argument build_vignettes=TRUE (Note: this will take considerably longer than building the package without the vignette).

Usage

Importing data

chromatographR can now import ChemStation and MassHunter files directly (using the Aston or Entab parsers wrapped by chromConverter) as well as regular csv and ascii files.

Analysis

Please see the vignette included with the package for details on the application of chromatographR for the analysis of HPLC data. A second vignette with a suggested workflow for the analysis of GC-FID data will be forthcoming soon.

Contributing

Contributions to the package are very welcome. Please get in touch (preferable by opening a GitHub issue) to discuss any suggestions or to file a bug report. Some good reasons to file an issue:

• You found an actual bug.
• You're getting a cryptic error message that you don't understand.
• You have a file format you'd like to read that isn't currently supported by chromatographR. (If you do this, please make sure to include a link to an example file!)
• You have a new feature you'd like to see implemented.

Citation:

If you use chromatographR in published work, please cite it as follows:

Bass, E. (2022). chromatographR: chromatographic data analysis toolset (version 0.4.4). https://cran.r-project.org/package=chromatographR/