In the flow diagram below, we visualized the functionality of GCalignR within a complete workflow of analysing chemical data. This vignette gives an quick introduction into using GCalignR, whereas a more detailed description of the background is found in our and in the second vignette of the package "GCalignR: How does the Algorithm work?". Furthermore, replicates that were analysed using both GC-MS and GC-FID with identical gas chromatography settings can be aligned together and may be used to identify peaks and validate alignment results.
Also, we recommend to double-check the resulting alignment with mass-spectrometry data, where available.
GCalignR has been created for situations where the main interest of the research is in exploring broader patterns rather then the specific function of a certain chemical, which is unlikely to be determined correctly in all cases when just retention times are used. In other words: The clearer the peaks are which were extracted from the chromatograms, the better the alignment will be. The implemented algorithm is purely based on retention time data, which is why the quality of the alignment is highly dependent on the quality of the raw data and the parameters used for the initial peak detection. peak height, peak area) that characterise each peak in a dataset. The input format of GCalignR is a peak list, which is comprised of retention times and arbitrary variables (e.g. Using sophisticated visualisations, the resulting alignments can then be fine tuned. GCalignR implements a fast and objective method to cluster putatively homologous substances prior to multivariate statistical analyses. We developed GCalignR primarily as an alignment tool for GC-FID data based on peak retention times, but other types of data that contain retention time information for peaks (e.g. Knitr ::opts_chunk $ set(cache = FALSE, fig.width = 8, fig.height = 8,highlight = TRUE,comment = "#>",strip.white = TRUE,collapse = TRUE, fig.align = "center", cache = F, warning = F, message = F) simple_chroma: Simulate simple chromatograms.remove_blanks: Remove peaks present in negative control samples.read_peak_list: Read content of a text file and convert it to a list.read_empower2: Import data from single EMPOWER2 HPLC files.print.GCalign: Summarising Peak Alignments with GCalignR.plot.GCalign: Plot diagnostics for an GCalign Object.peak_interspace: Estimate the observed space between peaks within.peak_factors: Grouping factors corresponding to gas-chromatography data of.peak_data: Gas-chromatography data for Antarctic Fur Seals.norm_peaks: Normalisation of peak abundancies.merge_redundant_rows: Merge redundant rows.
#HOW TO INSTALL PACKAGE IN R STEP BY STEP FULL#
linear_transformation: Full Alignment of Peak Lists by linear retention time.gc_heatmap: Visualises peak alignments in form of a heatmap.GCalignR: GCalignR: A Package to Align Gas Chromatography Peaks Based.
#HOW TO INSTALL PACKAGE IN R STEP BY STEP SERIES#