Package: GCalignR 1.0.7.1
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:
GCalignR_1.0.7.1.tar.gz
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GCalignR.pdf |GCalignR.html✨
GCalignR/json (API)
NEWS
| # 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
- 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
Last updated 2 months agofrom:397649f935. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 27 2024 |
| R-4.5-win | OK | Oct 27 2024 |
| R-4.5-linux | OK | Oct 27 2024 |
| R-4.4-win | OK | Oct 27 2024 |
| R-4.4-mac | OK | Oct 27 2024 |
| R-4.3-win | OK | Oct 27 2024 |
| R-4.3-mac | OK | Oct 27 2024 |
Exports:align_chromatogramscheck_inputchoose_optimal_referencedraw_chromatogramfind_peaksgc_heatmaplinear_transformationmerge_redundant_rowsnorm_peakspeak_interspaceread_empower2read_peak_listremove_blanksremove_singletonssimple_chroma
Dependencies:bitbit64clicliprcolorspacecpp11crayonfansifarverggplot2gluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepbapplypillarpkgconfigplyrprettyunitsprogressR6RColorBrewerRcppreadrreshape2rlangscalesstringistringrtibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
GCalignR Step by Step
Rendered fromGCalignR_step_by_step.Rmdusingknitr::rmarkdownon Oct 27 2024.Last update: 2024-07-03
Started: 2016-05-13
GCalignR: How does the Algorithms work?
Rendered fromGCalignR_How_does_the_Algorithm_work.Rmdusingknitr::rmarkdownon Oct 27 2024.Last update: 2020-08-20
Started: 2018-06-21
