Man pages for camilleroquencourt/ptairMS
Pre-processing PTR-TOF-MS Data
| aggregate | aggregate peakgroup for align function |
| align | Alignment with kernel gaussian density |
| alignSamples | Alignment between samples |
| annotation | Putative annotation of VOC mz by using the reference... |
| calibration | Calibrates the mass axis with references masses |
| calibrationFun | calibration function |
| changeTimeLimits | Shinny appplication to modify and view expiration limits This... |
| convert_to_mzML | Convert a h5 file to mzML |
| createPtrSet | Creates a ptrSet object form a directory |
| cumulative_fit_function | Create cumulative function fit |
| deadTimeCorr | Dead time correction on raw data |
| defineKnots | Define the knots location |
| detectPeak | Detection and quantification of peaks for a ptrSet object. |
| determinePeakShape | Determine peak shape from raw data in tof |
| exportSampleMetada | export sampleMetadata |
| extractEIC | extract all raw EIC from a pre-definied peak List |
| fit_averagePeak | Fit peak with average function |
| fit_averagePeak_function | fit function average |
| 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... |
| 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 |
| initializeFit | initialization for apply fit function in the spectrum |
| LocalMaximaSG | Find local maxima with Savitzky Golay filter |
| makeSubGroup | Use in align function. return a peak group thanks to kernel... |
| OptimalWindowsSG | Find optimal window's size for Savitzky Golay filter |
| PeakList | Detection and quantification of peaks on a sum spectrum. |
| plot | Plot a ptrSet object |
| plotCalib | Plot the calibration peaks after calibration |
| plotFeatures | Plot raw average spectrum around a mzRange |
| plotPeakShape | plot the average peak shape of reference calibration masses... |
| plotRaw | Plot method for 'ptrRaw' objects |
| plotTIC | plot the Total Ion sptectrum (TIC) for one or several files. |
| ptairMS-package | ptairMS: Pre-processing PTR-TOF-MS Data |
| ptrRaw | PTR-TOF-MS raw data from a rhdf5 file |
| ptrSet | 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... |
| rmPeakList | remove the peakList of an ptrSet object |
| RunShinnyApp | Graphical interface of ptairMS workflow |
| setSampleMetadata | set sampleMetadata in a ptrSet |
| show-ptrRaw-method | show a ptrRaw object |
| show-ptrSet-method | show a ptrSet object |
| snipBase | Baseline estimation |
| timeLimits | Calculates time limits on the breath tracer |
| TransmissionCurve | Estimation of the transmisison curve |
| updatePtrSet | update a ptrSet object |
| width | Calculate the FWHM (Full Width at Half Maximum) in raw data |
| writeEset | Exporting an ExpressionSet instance into 3 tabulated files... |
