proFIA: Preprocessing of FIA-HRMS data

Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and generate the peak table. The workflow includes noise modelling, band detection and filtering then signal matching and missing value imputation. The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.

AuthorAlexis Delabriere and Etienne Thevenot.
Date of publicationNone
MaintainerAlexis Delabriere <alexis.delabriere@cea.fr>
LicenseCeCILL
Version1.0.10

View on Bioconductor

Man pages

acquisitionDirectory: Create a table containg the classes of the acquisition.

analyzeAcquisitionFIA: Wrapper function for the full FIA analysis workflow.

determiningSizePeak.Geom: Determine the limits of the injection peak in a FIA...

estimateNoiseListFiles: Estimate the noise of multiple MS acquisition.

exportDataMatrix-proFIAset-method: Export data matrix.

exportExpressionSet-proFIAset-method: Export proFIAset to ExpressionSet

exportPeakTable-proFIAset-method: Export proFIAset as a peak table.

exportSampleMetadata-proFIAset-method: Export samples metadata.

exportVariableMetadata-proFIAset-method: Export variable metadata.

fillPeaks.WKNN-proFIAset-method: Fill missing values in the peak table.

findBandsFIA: Detect band in a FIA acquisition

findFIAsignal: Detect peaks in an FIA acquisition.

findMzGroup-proFIAset-method: find a group in a FIA experiment.

getInjectionPeak: Fit an injection peak to an FIA acquisition.

group.FIA-proFIAset-method: Group the peaks of an FIA acquisition.

makeDataMatrix-proFIAset-method: Construct the data matrix of a proFIAset object.

noiseEstimation-class: An S4 class to represent heteroscedasctic noise of MS.

peaksGroup-proFIAset-method: Return the peaks corresponding to a group.

plotEICs-proFIAset-method: Plot raw temporal profiles of the selected group.

plotInjectionPeaks-proFIAset-method: Plot the injection peaks of a proFIAset object.

plotNoise: Plot the estimated noise from a proFIAset object.

plotRaw-proFIAset-method: plotting of raw data

proFIA-package: Process FIA-HRMS datasets.

proFIAset: Process FIA experiment.

proFIAset-class: An S4 class to represent an FIA experiments.

Functions

acquisitionDirectory Man page
analyzeAcquisitionFIA Man page
dataMatrix Man page
dataMatrix,proFIAset-method Man page
determiningSizePeak Man page
determiningSizePeak.Geom Man page
estimateNoiseListFiles Man page
exportDataMatrix Man page
exportDataMatrix,proFIAset-method Man page
exportExpressionSet Man page
exportExpressionSet,proFIAset-method Man page
exportPeakTable Man page
exportPeakTable,proFIAset-method Man page
exportSampleMetadata Man page
exportSampleMetadata,proFIAset-method Man page
exportVariableMetadata Man page
exportVariableMetadata,proFIAset-method Man page
fillPeaks.WKNN Man page
fillPeaks.WKNN,proFIAset-method Man page
findBandsFIA Man page
findFIASignal Man page
findMzGroup Man page
findMzGroup,proFIAset-method Man page
findPeaks Man page
getInjectionPeak Man page
group.FIA Man page
group.FIA,proFIAset-method Man page
groupMatrix Man page
groupMatrix,proFIAset-method Man page
injectionPeaks Man page
injectionPeaks,proFIAset-method Man page
makeDataMatrix Man page
makeDataMatrix,proFIAset-method Man page
noiseEstimation-class Man page
peaks Man page
peaksGroup Man page
peaksGroup,proFIAset-method Man page
peaks,proFIAset-method Man page
phenoClasses Man page
phenoClasses,proFIAset-method Man page
plotEICs Man page
plotEICs,proFIAset-method Man page
plotInjectionPeaks Man page
plotInjectionPeaks,proFIAset-method Man page
plotNoise Man page
plotRaw Man page
plotRaw,proFIAset-method Man page
proFIA Man page
proFIA-package Man page
proFIAset Man page
proFIAset-class Man page

Files

proFIA/.BBSoptions
proFIA/DESCRIPTION
proFIA/NAMESPACE
proFIA/NEWS
proFIA/R
proFIA/R/Denoising.R proFIA/R/cWrapper.R proFIA/R/classContainer.R proFIA/R/fastMatchPpm.R proFIA/R/findPeaksFIA.R proFIA/R/methodsContainer.R proFIA/R/noiseEstimator.R proFIA/R/proFIA-package.R
proFIA/build
proFIA/build/vignette.rds
proFIA/inst
proFIA/inst/CITATION
proFIA/inst/NEWS
proFIA/inst/doc
proFIA/inst/doc/proFIA-vignette.R
proFIA/inst/doc/proFIA-vignette.Rmd
proFIA/inst/doc/proFIA-vignette.html
proFIA/inst/unitTests
proFIA/inst/unitTests/test_proFIA.R
proFIA/man
proFIA/man/acquisitionDirectory.Rd proFIA/man/analyzeAcquisitionFIA.Rd proFIA/man/determiningSizePeak.Geom.Rd proFIA/man/estimateNoiseListFiles.Rd proFIA/man/exportDataMatrix-proFIAset-method.Rd proFIA/man/exportExpressionSet-proFIAset-method.Rd proFIA/man/exportPeakTable-proFIAset-method.Rd proFIA/man/exportSampleMetadata-proFIAset-method.Rd proFIA/man/exportVariableMetadata-proFIAset-method.Rd proFIA/man/fillPeaks.WKNN-proFIAset-method.Rd proFIA/man/findBandsFIA.Rd proFIA/man/findFIAsignal.Rd proFIA/man/findMzGroup-proFIAset-method.Rd proFIA/man/getInjectionPeak.Rd proFIA/man/group.FIA-proFIAset-method.Rd proFIA/man/makeDataMatrix-proFIAset-method.Rd proFIA/man/noiseEstimation-class.Rd proFIA/man/peaksGroup-proFIAset-method.Rd proFIA/man/plotEICs-proFIAset-method.Rd proFIA/man/plotInjectionPeaks-proFIAset-method.Rd proFIA/man/plotNoise.Rd proFIA/man/plotRaw-proFIAset-method.Rd proFIA/man/proFIA-package.Rd proFIA/man/proFIAset-class.Rd proFIA/man/proFIAset.Rd
proFIA/src
proFIA/src/FIABandsExtractionCentroid.c
proFIA/src/UtilFunc.c
proFIA/src/UtilFunc.h
proFIA/src/fastMatchPpm.c
proFIA/tests
proFIA/tests/runTests.R
proFIA/vignettes
proFIA/vignettes/proFIA-vignette.Rmd
proFIA/vignettes/proFIA-vignette.bib
proFIA/vignettes/workflow_info.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.