README.md

GCalignR

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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.

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

Installing GCalignR:

The most recent version on GitHub introduces the new parameter remove_empty within the align_chromatograms function. This parameter allows to remove empty samples (i.e. no peak is left after the processing) from the dataset. Otherwise issues with downstream analyses can occur

    if (!("devtools" %in% rownames(installed.packages()))) { 
    install.packages("devtools")
    } else if (packageVersion("devtools") < 1.6) {
    install.packages("devtools")
    }
    devtools::install_github("mottensmann/GCalignR@v1.0.3", build_vignettes = TRUE)
install.packages("GCalignR", dependencies = T)

Get started with GCalignR

To get started read the vignettes:

browseVignettes("GCalignR")

If you encounter bugs or if you have any suggestions for improvement (for instance on how to speed up the algorithm!), 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 simplify this process please send a short description of the problem along with the code you have been using as a script file (.R) together with a minimal example input file (.txt).

Reference

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



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GCalignR documentation built on Aug. 26, 2020, 9:06 a.m.