Package: GCIMS 0.1.1
GCIMS: Pre-processing for GC-IMS data
A package for the analysis of ion mobility spectrometry (IMS) measurements, as well as samples from multicapillary columns coupled with IMS (MCC-IMS) and gas chromatography coupled to ion mobility spectrometry (GC-IMS). The package provides a complete workflow for the analysis, importing the data, preprocessing the spectra as well as classification and regression techniques for the modelling of the spectra. The package also includes visualization helpers, to represent topographic plots, extracted and total ion chromatograms and IMS spectra.
Authors:
GCIMS_0.1.1.tar.gz
GCIMS_0.1.1.zip(r-4.5)GCIMS_0.1.1.zip(r-4.4)GCIMS_0.1.1.zip(r-4.3)
GCIMS_0.1.1.tgz(r-4.4-any)GCIMS_0.1.1.tgz(r-4.3-any)
GCIMS_0.1.1.tar.gz(r-4.5-noble)GCIMS_0.1.1.tar.gz(r-4.4-noble)
GCIMS_0.1.1.tgz(r-4.4-emscripten)GCIMS_0.1.1.tgz(r-4.3-emscripten)
GCIMS.pdf |GCIMS.html✨
GCIMS/json (API)
NEWS
| # Install 'GCIMS' in R: |
| install.packages('GCIMS', repos = c('https://zeehio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sipss/gcims/issues
softwarepreprocessingvisualizationclassificationcheminformaticsmetabolomicsdataimport
Last updated 22 hours agofrom:beef75b4cf. Checks:OK: 1 NOTE: 6. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | NOTE | Nov 18 2024 |
| R-4.5-linux | NOTE | Nov 18 2024 |
| R-4.4-win | NOTE | Nov 18 2024 |
| R-4.4-mac | NOTE | Nov 18 2024 |
| R-4.3-win | NOTE | Nov 18 2024 |
| R-4.3-mac | NOTE | Nov 18 2024 |
Exports:add_peaklist_rectalignalignDtalignPlotsalignRt_ipalignRt_powalignRt_ptwbaselinebaseline<-clusterPeakscreate_annotations_tablecubic_root_transdecimateDelayedOperationdescriptiondescription<-download_three_ketones_datasetdtimeestimateBaselinefilterDtfilterRtfindPeaksGCIMSChromatogramGCIMSDatasetGCIMSDataset_fromListGCIMSSampleGCIMSSpectrumgetChromatogramgetRICgetSamplegetSpectrumgetTISimputePeakTableintegratePeaksintensityintensity<-omit_timesoverlay_peaklistpDatapData<-peakspeaks<-peakTableplotplot_interactiveplotRawplotRICplotTISprealignread_mearealizertimesampleNamessampleNames<-show_progress_barsmoothupdateObject
Dependencies:BHBiobaseBiocGenericsBiocParallelcliclustercodetoolscolorspacecpp11digestdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsggplot2gluegtableisobandlabelinglambda.rlatticelifecyclemagrittrMASSMassSpecWaveletMatrixmdendromgcvmunsellnlmepillarpkgconfigplyrProtGenericsptwpurrrR6RColorBrewerRcppRcppArmadilloRcppDEreshape2rlangS4Vectorsscalessgolaysignalsnowstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithryaml
Creating a workflow step
Rendered fromcreating-a-workflow-step.Rmdusingknitr::rmarkdownon Nov 18 2024.Last update: 2023-12-05
Started: 2022-11-29
Importing custom data formats
Rendered fromimporting-custom-data-formats.Rmdusingknitr::rmarkdownon Nov 18 2024.Last update: 2023-03-31
Started: 2023-02-23
Introduction to GCIMS
Rendered fromintroduction-to-gcims.Rmdusingknitr::rmarkdownon Nov 18 2024.Last update: 2024-05-06
Started: 2022-01-10
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add peak list rectangles to a raw plot | add_peaklist_rect |
| Align a GCIMS dataset | align,GCIMSDataset-method |
| Align a GCIMSSample object, in retention time | align,GCIMSSample-method |
| Align a GCIMSSample in drift time with a multiplicative correction | alignDt |
| Plots to interpret alignment results | alignPlots |
| Align a GCIMSSample in retention time with a multiplicative correction | alignRt_ip |
| Align a GCIMSSample in retention time with parametric optimized warping | alignRt_pow |
| Align a GCIMSSample in retention time using parametric time warping | alignRt_ptw |
| Turn the intensity matrix into a data frame | as.data.frame.GCIMSSample |
| Group peaks in clusters | clusterPeaks |
| Create a table for defining dataset annotations | create_annotations_table |
| Cubic root transformation | cubic_root_trans |
| Decimate a GCIMS dataset keeping 1 out of n points | decimate,GCIMSDataset-method |
| Decimates a GCIMS sample | decimate,GCIMSSample-method |
| Create a DelayedOperation object | DelayedOperation |
| Delayed Operation class | DelayedOperation-class |
| Download three samples (6-ketone mixture) | download_three_ketones_dataset |
| Get the drift time of the chromatogram | dtime,GCIMSChromatogram-method |
| Get A reference drift time vector for the dataset | dtime,GCIMSDataset-method |
| Estimate the baseline of a GCIMS Chromatogram using a connect local minima algorithm | baseline,GCIMSChromatogram-method baseline<-,GCIMSChromatogram-method estimateBaseline,GCIMSChromatogram-method |
| Estimate the baseline of a GCIMS Sample using a connect local minima algorithm | estimateBaseline,GCIMSDataset-method |
| Estimate the baseline of a GCIMS Sample using a connect local minima algorithm | baseline,GCIMSSample-method baseline<-,GCIMSSample-method estimateBaseline,GCIMSSample-method |
| Estimate the baseline of a GCIMS Spectrum using a connect local minima algorithm | baseline,GCIMSSpectrum-method baseline<-,GCIMSSpectrum-method estimateBaseline,GCIMSSpectrum-method |
| Filter GCIMSDataset samples by drift time | filterDt,GCIMSDataset-method |
| Filter GCIMSSample samples by drift time | filterDt,GCIMSSample-method |
| Filter GCIMSDataset samples by retention time | filterRt,GCIMSDataset-method |
| Filter GCIMSSample samples by retention time | filterRt,GCIMSSample-method |
| Find Peaks in an object | findPeaks |
| Peak detection for a GCIMSChromatogram | findPeaks,GCIMSChromatogram-method |
| Peak detection on the GCIMS dataset | findPeaks,GCIMSDataset-method |
| Peak detection for a GCIMSSample | findPeaks,GCIMSSample-method |
| Peak detection for a GCIMSSpectrum | findPeaks,GCIMSSpectrum-method |
| GCIMS Generics | align baseline baseline<- decimate dtime estimateBaseline filterDt GCIMS-generics getRIC getTIS integratePeaks plotRIC plotTIS prealign |
| Create a GCIMSChromatogram object | GCIMSChromatogram |
| GCIMSChromatogram class | as.data.frame.GCIMSChromatogram description,GCIMSChromatogram-method description<-,GCIMSChromatogram,ANY-method GCIMSChromatogram-class peaks,GCIMSChromatogram-method peaks<-,GCIMSChromatogram-method plot,GCIMSChromatogram,ANY-method |
| GCIMSDataset | GCIMSDataset GCIMSDataset-class |
| GCIMSDataset_fromList | GCIMSDataset_fromList |
| Create a GCIMSSample object | GCIMSSample |
| GCIMSSample class | GCIMSSample-class |
| Methods for the GCIMSSample class | description,GCIMSSample-method description<-,GCIMSSample,ANY-method dim.GCIMSSample GCIMSSample-methods peaks,GCIMSSample-method peaks<-,GCIMSSample-method subset subset.GCIMSSample [.GCIMSSample |
| Drift time, Retention time, Intensity of GCIMSSamples | dtime,GCIMSSample-method GCIMSSample-rtime-dtime-intensity intensity,GCIMSSample-method intensity<-,GCIMSSample-method rtime,GCIMSSample-method |
| GCIMSSpectrum class | description,GCIMSSpectrum-method description<-,GCIMSSpectrum,ANY-method dtime,GCIMSSpectrum-method GCIMSSpectrum GCIMSSpectrum-class intensity,GCIMSSpectrum-method peaks,GCIMSSpectrum-method peaks<-,GCIMSSpectrum-method plot,GCIMSSpectrum,ANY-method rtime,GCIMSSpectrum-method |
| Get the extracted ion chromatogram | getChromatogram |
| Get Reverse Ion Chromatogram | getRIC,GCIMSDataset-method |
| Get the reverse ion chromatogram | getRIC,GCIMSSample-method |
| Get IMS spectrum from a sample | getSpectrum |
| Get Total Ion Spectra matrix | getTIS,GCIMSDataset-method |
| Get the total ion spectrum | getTIS,GCIMSSample-method |
| Impute a Peak table | imputePeakTable |
| Integrate peaks in a GCIMSDataset | integratePeaks,GCIMSDataset-method |
| Peak integration for a GCIMSSample | integratePeaks,GCIMSSample-method |
| Get the intensity vector | intensity,GCIMSChromatogram-method |
| Omit ROIs present in certain retention and drift times | omit_times |
| Overlay a peak list to a plot | overlay_peaklist |
| Get/Set the phenotype data | pData,GCIMSDataset-method pData<-,GCIMSDataset,ANY-method |
| Get the peak list | peaks,GCIMSDataset-method peaks<-,GCIMSDataset-method |
| Build a peak table | peakTable |
| Make a plot interactive | plot_interactive |
| Topographical plot of a GCIMSSample object | plot,GCIMSSample,ANY-method |
| Plot Reverse Ion Chromatograms | plotRIC,GCIMSDataset-method |
| Plot Total Ion Spectra | plotTIS,GCIMSDataset-method |
| Align a GCIMSSample object, in drift time and to the injection point in retention time | prealign,GCIMSSample-method |
| Read .mea files (from GAS Dortmund) | read_mea |
| Runs all delayed operations on the object | realize |
| Get the retention time vector | rtime,GCIMSChromatogram-method |
| Get a reference retention time vector for the dataset | rtime,GCIMSDataset-method |
| Sample names | sampleNames,GCIMSDataset-method sampleNames<-,GCIMSDataset,ANY-method |
| Show progress bar | show_progress_bar |
| Smoothing a GCIMS chromatogram using a Savitzky-Golay filter | smooth,GCIMSChromatogram-method |
| Smoothing a GCIMS dataset using a Savitzky-Golay filter | smooth,GCIMSDataset-method |
| Smoothing a GCIMS sample using a Savitzky-Golay filter | smooth,GCIMSSample-method |
| Smoothing a GCIMS Spectrum using a Savitzky-Golay filter | smooth,GCIMSSpectrum-method |
| Updates old saved GCIMSSample object to the latest version | updateObject,GCIMSSample-method |
