# Pre-processing PTR-TOF-MS Data

## Documentation for package ‘ptairMS’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'