Pre-processing PTR-TOF-MS Data

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Documentation for package ‘ptairMS’ version 1.13.0

• 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.
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
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
RunShinnyApp	Graphical interface of ptairMS workflow
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'