| aggregate | aggregate peakgroup for align function |
| alignSamples | Alignment between samples |
| alignSamples-method | Alignment between samples |
| annotateVOC | Putative annotation of VOC mz by using the reference compilation from the literature |
| annotateVOC-method | Putative annotation of VOC mz by using the reference compilation from the literature |
| calibration | Calibrates the mass axis with references masses |
| calibration-method | Calibrates the mass axis with references masses |
| changeTimeLimits | Shinny appplication to modify and view expiration limits This function run a shiny app, where you can check the automatic expiration detection, knots location, and modify it. |
| convert_to_mzML | Convert a h5 file to mzML |
| createPtrSet | Creates a ptrSet object form a directory |
| defineKnots | Define the knots location |
| defineKnots-method | Define the knots location |
| detectPeak | Detection and quantification of peaks for a ptrSet object. |
| detectPeak-method | Detection and quantification of peaks for a ptrSet object. |
| exhaledPtrset | PtrSet of the exhaled air rdhf 5 files |
| exportSampleMetada | export sampleMetadata |
| formula2mass | Compute exact mass. |
| getDirectory | get the files directory of a ptrSet |
| getFileNames | get the file names containing in the directory of a ptrSet or ptrRaw |
| getFileNames-method | get the file names containing in the directory of a ptrSet or ptrRaw |
| getPeakList | get the peak list of a ptrSet object |
| getSampleMetadata | get sampleMetadata of a ptrSet |
| importSampleMetadata | import a sampleMetadata from a tsv file to a ptrSet object |
| impute | Imputes the missing values |
| imputeMat | Impute missing values on an matrix set from an ptrSet |
| LocalMaximaSG | Find local maxima with Savitzky Golay filter |
| mycobacteriaSet | PtrSet of the mycobacteria rdhf 5 files |
| PeakList | Detection and quantification of peaks on a sum spectrum. |
| PeakList-method | Detection and quantification of peaks on a sum spectrum. |
| plot-method | Plot a ptrSet object |
| plot.ptrSet | Plot a ptrSet object |
| plotCalib | Plot the calibration peaks after calibration |
| plotCalib-method | Plot the calibration peaks after calibration |
| plotFeatures | Plot raw average spectrum around a mzRange |
| plotFeatures-method | Plot raw average spectrum around a mzRange |
| plotRaw | Plot method for 'ptrRaw' objects |
| plotRaw-method | Plot method for 'ptrRaw' objects |
| plotTIC | plot the Total Ion sptectrum (TIC) for one or several files. |
| plotTIC-method | plot the Total Ion sptectrum (TIC) for one or several files. |
| ptrRaw-class | PTR-TOF-MS raw data from a rhdf5 file |
| ptrSet-class | A set of PTR-TOF-MS raw data informations |
| readRaw | Read a h5 file of PTR-TOF-MS data |
| resetSampleMetadata | reset the default sampleMetadata, containing the suborders names and the acquisition dates as columns. |
| rmPeakList | remove the peakList of an ptrSet object |
| setSampleMetadata | set sampleMetadata in a ptrSet |
| show-method | show a ptrRaw object |
| show-method | show a ptrSet object |
| timeLimits | Calculates time limits on the breath tracer |
| timeLimits-method | Calculates time limits on the breath tracer |
| updatePtrSet | update a ptrSet object |
| writeEset | Exporting an ExpressionSet instance into 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', and 'variableMetadata.tsv' |
| writeEset-method | Exporting an ExpressionSet instance into 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', and 'variableMetadata.tsv' |