Package: GCalignR 1.0.7.2

GCalignR: Simple Peak Alignment for Gas-Chromatography Data

Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.

Authors:Meinolf Ottensmann [aut, cre], Martin Stoffel [aut], Hazel J. Nichols [aut], Joseph I. Hoffman [aut]

GCalignR_1.0.7.2.tar.gz
GCalignR_1.0.7.2.zip(r-4.7-any)GCalignR_1.0.7.2.zip(r-4.6-any)GCalignR_1.0.7.2.zip(r-4.5-any)
GCalignR_1.0.7.2.tgz(r-4.6-any)GCalignR_1.0.7.2.tgz(r-4.5-any)
GCalignR_1.0.7.2.tar.gz(r-4.7-any)GCalignR_1.0.7.2.tar.gz(r-4.6-any)
GCalignR_1.0.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GCalignR/json (API)

# Install 'GCalignR' in R:
install.packages('GCalignR', repos = c('https://mottensmann.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mottensmann/gcalignr/issues

Datasets:
  • aligned_peak_data - Aligned Gas-Chromatography data
  • peak_data - Gas-chromatography data for Antarctic Fur Seals
  • peak_factors - Grouping factors corresponding to gas-chromatography data of Antarctic Fur Seals

On CRAN:

Conda:

6.19 score 6 stars 43 scripts 411 downloads 3 mentions 15 exports 39 dependencies

Last updated from:1ec14140d9. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK167
source / vignettesOK239
linux-releaseOK164
macos-releaseOK225
macos-oldrelOK202
windows-develOK90
windows-releaseOK124
windows-oldrelOK84
wasm-releaseOK108

Exports:align_chromatogramscheck_inputchoose_optimal_referencedraw_chromatogramfind_peaksgc_heatmaplinear_transformationmerge_redundant_rowsnorm_peakspeak_interspaceread_empower2read_peak_listremove_blanksremove_singletonssimple_chroma

Dependencies:bitbit64clicliprcpp11crayonfarverggplot2gluegtablehmsisobandlabelinglifecyclemagrittrpbapplypillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreadrreshape2rlangS7scalesstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithr

GCalignR Step by Step
Introduction | GCalignR workflow in a larger context | Installation | The functions below form the core of GCalignR: | The alignment algorithm | Optional steps: | Input data | Alternative input from R | GCalignR workflow | Check the input | Align chromatograms | Visual diagnostics for the aligned data | Normalise peaks and log+1 transformation | Visualise patterns by ordination plots using the vegan package | Non-metric multidimensional scaling | Multivariate analysis using adonis2 | References
Rendered fromGCalignR_step_by_step.Rmdusingknitr::rmarkdown

Last update: 2024-07-03
Started: 2016-05-13

GCalignR: How does the Algorithms work?
Introduction | What´s a Peak List and how to create one ? | Aligning peak lists | Full alignment of peaks lists | Partial alignment of peaks | Merging rows | Aligning the a hypothetical dataset | Remarks | References
Rendered fromGCalignR_How_does_the_Algorithm_work.Rmdusingknitr::rmarkdown

Last update: 2020-08-20
Started: 2018-06-21

Readme and manuals

Help Manual

Help pageTopics
Aligning peaks based on retention timesalign_chromatograms
Aligned Gas-Chromatography dataaligned_peak_data
Output aligned data in form of a data frame for each variableas.data.frame.GCalign
Subtraction of blank readings from sample readingsblank_substraction
Check input prior to processing in GCalignRcheck_input
Select the optimal reference for full alignments of peak listschoose_optimal_reference
Visualise peak lists as a pseudo-chromatogramdraw_chromatogram
Detect local maxima in time seriesfind_peaks
Visualises peak alignments in form of a heatmapgc_heatmap
GCalignR: A Package to Align Gas Chromatography Peaks Based on Retention TimesGCalignR-package GCalignR
Full Alignment of Peak Lists by linear retention time correction.linear_transformation
Merge redundant rowsmerge_redundant_rows
Normalisation of peak abundanciesnorm_peaks
Gas-chromatography data for Antarctic Fur Seals (_Arctocephalus gazella_)peak_data
Grouping factors corresponding to gas-chromatography data of Antarctic Fur Seals (_Arctocephalus gazella_)peak_factors
Estimate the observed space between peaks within chromatogramspeak_interspace
Plot diagnostics for an GCalign Objectplot.GCalign
Summarising Peak Alignments with GCalignRprint.GCalign
Import data from single EMPOWER2 HPLC filesread_empower2
Read content of a text file and convert it to a listread_peak_list
Remove peaks present in negative control samplesremove_blanks
Remove singletonsremove_singletons
Simulate simple chromatogramssimple_chroma