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GCalignR

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

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

• Row 1: Sample names
• Row 2: Variable names
• Row 3-N: GC data
  • Each block belongs to a sample as shown for sample A (green) andsample B (orange) above

Installing GCalignR:

The latest release v1.0.6 is onCRAN.Click herefor an overview of past releases and a brief description of appliedchanges.

install.packages("GCalignR",dependencies = T)

The current developmental version is identical to the CRANrelease

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

Get started with GCalignR

To get started read the vignettes:

browseVignettes("GCalignR")

Basic usage of the main function to align peaks:

• data: Path to a text file (see input format above), orlist of data frames, each corresponding to a sample
• rt_col_name: column name of retention time values
• max_linear_shift: Here, no adjustment of systematiclinear drift
• max_diff_peak2mean: Here, sort all peaks strictly byretention time
• min_diff_peak2peak: Here, try to merge peaks when rtdiffers by less than 0.1

library(GCalignR)#> Warning: package 'GCalignR' was built under R version 4.4.1

aligned<-align_chromatograms(data = peak_data[1:4],# list of data framert_col_name ="time",# retention timemax_linear_shift =0,#max_diff_peak2mean =0,min_diff_peak2peak =0.08)#> Run GCalignR#> Start: 2024-07-03 14:53:38#>#> Data for 4 samples loaded.#> No reference was specified. Hence, a reference will be selected automatically ...#>#> 'C2' was selected on the basis of highest average similarity to all samples (score = 0.06).#> Start correcting linear shifts with "C2" as a reference ...#>#> Start aligning peaks ...  this might take a while!#>#> Merge redundant rows ...#>#> Alignment completed!#> Time: 2024-07-03 14:53:41

The parameter values above differ from the defaults shown inthe paper and the package vignette. In a nutshell, we now suggest inmost cases to setmax_diff_peak2mean = 0. This way peaksare first simply sorted based on the given retention time value and thenpurelymin_diff_peak2peak specifies which peaks will beevaluated for a merge. Additionally, this enables the possibility for aconsiderable boost in computation speed of the first alignment steps(available since version 1.0.5, currently only on GitHub!)

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

Published paper

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

#> Warning: package 'ggplot2' was built under R version 4.4.1