Package index • GCIMS

All functions
`DelayedOperation-class`	Delayed Operation class
`DelayedOperation()`	Create a DelayedOperation object
`dtime()` `getTIS()` `getRIC()` `plotTIS()` `plotRIC()` `filterDt()` `decimate()` `align()` `prealign()` `estimateBaseline()` `baseline()` `baseline<-`() `integratePeaks()`	GCIMS Generics
`as.data.frame(<GCIMSChromatogram>)` `description(<GCIMSChromatogram>)` `description<-`(<GCIMSChromatogram>,<ANY>) `peaks(<GCIMSChromatogram>)` `peaks<-`(<GCIMSChromatogram>) `plot(<GCIMSChromatogram>,<ANY>)`	GCIMSChromatogram class
`GCIMSChromatogram()`	Create a GCIMSChromatogram object
`GCIMSDataset` `GCIMSDataset-class`	GCIMSDataset
`GCIMSDataset_fromList()`	GCIMSDataset_fromList
`GCIMSSample-class`	GCIMSSample class
`[`(<GCIMSSample>) `dim(<GCIMSSample>)` `subset(<GCIMSSample>)` `description(<GCIMSSample>)` `description<-`(<GCIMSSample>,<ANY>) `peaks(<GCIMSSample>)` `peaks<-`(<GCIMSSample>)	Methods for the GCIMSSample class
`dtime(<GCIMSSample>)` `rtime(<GCIMSSample>)` `intensity(<GCIMSSample>)` `intensity<-`(<GCIMSSample>)	Drift time, Retention time, Intensity of GCIMSSamples
`GCIMSSample()`	Create a GCIMSSample object
`GCIMSSpectrum()` `description(<GCIMSSpectrum>)` `description<-`(<GCIMSSpectrum>,<ANY>) `dtime(<GCIMSSpectrum>)` `rtime(<GCIMSSpectrum>)` `intensity(<GCIMSSpectrum>)` `peaks(<GCIMSSpectrum>)` `peaks<-`(<GCIMSSpectrum>) `plot(<GCIMSSpectrum>,<ANY>)`	GCIMSSpectrum class
`add_peaklist_rect()`	Add peak list rectangles to a raw plot
`align(<GCIMSDataset>)`	Align a GCIMS dataset
`align(<GCIMSSample>)`	Align a GCIMSSample object, in retention time
`alignDt()`	Align a GCIMSSample in drift time with a multiplicative correction
`alignPlots()`	Plots to interpret alignment results
`alignRt_ip()`	Align a GCIMSSample in retention time with a multiplicative correction
`alignRt_pow()`	Align a GCIMSSample in retention time with parametric optimized warping
`alignRt_ptw()`	Align a GCIMSSample in retention time using parametric time warping
`as.data.frame(<GCIMSSample>)`	Turn the intensity matrix into a data frame
`clusterPeaks()`	Group peaks in clusters
`create_annotations_table()`	Create a table for defining dataset annotations
`cubic_root_trans()`	Cubic root transformation
`decimate(<GCIMSDataset>)`	Decimate a GCIMS dataset keeping 1 out of n points
`decimate(<GCIMSSample>)`	Decimates a GCIMS sample
`download_three_ketones_dataset()`	Download three samples (6-ketone mixture)
`dtime(<GCIMSChromatogram>)`	Get the drift time of the chromatogram
`dtime(<GCIMSDataset>)`	Get A reference drift time vector for the dataset
`estimateBaseline(<GCIMSChromatogram>)` `baseline(<GCIMSChromatogram>)` `baseline<-`(<GCIMSChromatogram>)	Estimate the baseline of a GCIMS Chromatogram using a connect local minima algorithm
`estimateBaseline(<GCIMSDataset>)`	Estimate the baseline of a GCIMS Sample using a connect local minima algorithm
`estimateBaseline(<GCIMSSample>)` `baseline(<GCIMSSample>)` `baseline<-`(<GCIMSSample>)	Estimate the baseline of a GCIMS Sample using a connect local minima algorithm
`estimateBaseline(<GCIMSSpectrum>)` `baseline(<GCIMSSpectrum>)` `baseline<-`(<GCIMSSpectrum>)	Estimate the baseline of a GCIMS Spectrum using a connect local minima algorithm
`filterDt(<GCIMSDataset>)`	Filter GCIMSDataset samples by drift time
`filterDt(<GCIMSSample>)`	Filter GCIMSSample samples by drift time
`filterRt(<GCIMSDataset>)`	Filter GCIMSDataset samples by retention time
`filterRt(<GCIMSSample>)`	Filter GCIMSSample samples by retention time
`findPeaks(<GCIMSChromatogram>)`	Peak detection for a GCIMSChromatogram
`findPeaks(<GCIMSDataset>)`	Peak detection on the GCIMS dataset
`findPeaks(<GCIMSSample>)`	Peak detection for a GCIMSSample
`findPeaks(<GCIMSSpectrum>)`	Peak detection for a GCIMSSpectrum
`findPeaks()`	Find Peaks in an object
`getChromatogram()`	Get the extracted ion chromatogram
`getRIC(<GCIMSDataset>)`	Get Reverse Ion Chromatogram
`getRIC(<GCIMSSample>)`	Get the reverse ion chromatogram
`getSpectrum()`	Get IMS spectrum from a sample
`getTIS(<GCIMSDataset>)`	Get Total Ion Spectra matrix
`getTIS(<GCIMSSample>)`	Get the total ion spectrum
`imputePeakTable()`	Impute a Peak table
`integratePeaks(<GCIMSDataset>)`	Integrate peaks in a GCIMSDataset
`integratePeaks(<GCIMSSample>)`	Peak integration for a GCIMSSample
`intensity(<GCIMSChromatogram>)`	Get the intensity vector
`omit_times()`	Omit ROIs present in certain retention and drift times
`overlay_peaklist()`	Overlay a peak list to a plot
`pData(<GCIMSDataset>)` `pData<-`(<GCIMSDataset>,<ANY>)	Get/Set the phenotype data
`peakTable()`	Build a peak table
`peaks(<GCIMSDataset>)` `peaks<-`(<GCIMSDataset>)	Get the peak list
`plot(<GCIMSSample>,<ANY>)`	Topographical plot of a GCIMSSample object
`plotRIC(<GCIMSDataset>)`	Plot Reverse Ion Chromatograms
`plotTIS(<GCIMSDataset>)`	Plot Total Ion Spectra
`plot_interactive()`	Make a plot interactive
`prealign(<GCIMSSample>)`	Align a GCIMSSample object, in drift time and to the injection point in retention time
`read_mea()`	Read .mea files (from GAS Dortmund)
`realize()`	Runs all delayed operations on the object
`rtime(<GCIMSChromatogram>)`	Get the retention time vector
`rtime(<GCIMSDataset>)`	Get a reference retention time vector for the dataset
`sampleNames(<GCIMSDataset>)` `sampleNames<-`(<GCIMSDataset>,<ANY>)	Sample names
`show_progress_bar()`	Show progress bar
`smooth(<GCIMSChromatogram>)`	Smoothing a GCIMS chromatogram using a Savitzky-Golay filter
`smooth(<GCIMSDataset>)`	Smoothing a GCIMS dataset using a Savitzky-Golay filter
`smooth(<GCIMSSample>)`	Smoothing a GCIMS sample using a Savitzky-Golay filter
`smooth(<GCIMSSpectrum>)`	Smoothing a GCIMS Spectrum using a Savitzky-Golay filter
`updateObject(<GCIMSSample>)`	Updates old saved GCIMSSample object to the latest version

Reference

All functions