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GCalignR provides simple functions to align peak lists obtained from Gas Chromatography Flame Ionization Detectors (GC-FID) based on retention times and plots to evaluate the quality of the alignment. The package supports any other one-dimensional chromatograpy technique that enables the user to create a peak list with at least one column specifying retention times as illustrated below.

plot of chunk unnamed-chunk-2

A short note on the input format

As with many software you need to get used to the input format which is shown in the illustration:

Installing GCalignR:

install.packages("GCalignR", dependencies = T)
    if (!("devtools" %in% rownames(installed.packages()))) { 
    } else if (packageVersion("devtools") < 1.6) {
    devtools::install_github("mottensmann/GCalignR", build_vignettes = TRUE)

Get started with GCalignR

To get started read the vignettes:


If you encounter bugs or if you have any suggestions for improvement, just contact meinolf.ottensmann[at]web.de

Also I´m happy to provide help if you can´t get it to work. Usually it is easy to solve small problems. However, in order to simplifiy this process please send a short describton of the problem along with the code you have been using as a script file (.R) together with a minimal example input file (.txt).


Ottensmann M, Stoffel MA, Nichols HJ, Hoffman JI (2018) GCalignR: An R package for aligning gas-chromatography data for ecological and evolutionary studies. PLoS ONE 13(6): e0198311. https://doi.org/10.1371/journal.pone.0198311