Package: ptairMS 1.13.0

camille Roquencourt

ptairMS: Pre-processing PTR-TOF-MS Data

This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a singl<e ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and quantification, feature alignment, missing value imputation and feature annotation. Applications to exhaled air and cell culture in headspace are described in the vignettes and examples. This package was used for data analysis of Gassin Delyle study on adults undergoing invasive mechanical ventilation in the intensive care unit due to severe COVID-19 or non-COVID-19 acute respiratory distress syndrome (ARDS), and permit to identfy four potentiel biomarquers of the infection.

Authors:camille Roquencourt [aut, cre]

ptairMS_1.13.0.tar.gz
ptairMS_1.13.0.zip(r-4.5)ptairMS_1.13.0.zip(r-4.4)ptairMS_1.13.0.zip(r-4.3)
ptairMS_1.13.0.tgz(r-4.4-arm64)ptairMS_1.13.0.tgz(r-4.4-x86_64)ptairMS_1.13.0.tgz(r-4.3-arm64)ptairMS_1.13.0.tgz(r-4.3-x86_64)
ptairMS_1.13.0.tar.gz(r-4.5-noble)ptairMS_1.13.0.tar.gz(r-4.4-noble)
ptairMS_1.13.0.tgz(r-4.4-emscripten)ptairMS_1.13.0.tgz(r-4.3-emscripten)
ptairMS.pdf |ptairMS.html✨
ptairMS/json (API)
NEWS

# Install 'ptairMS' in R:
install.packages('ptairMS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/camilleroquencourt/ptairms/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:ptairMS-1.13.0(bioc 3.20)ptairMS-1.12.0(bioc 3.19)

bioconductor-package

33 exports 0.71 score 189 dependencies

Last updated 2 months agofrom:f9cbcc5a04

Exports:alignSamplesannotateVOCcalibrationchangeTimeLimitsconvert_to_mzMLcreatePtrSetdefineKnotsdetectPeakexportSampleMetadaformula2massgetDirectorygetFileNamesgetPeakListgetSampleMetadataimportSampleMetadataimputeimputeMatLocalMaximaSGPeakListplotplotCalibplotFeaturesplotRawplotTICreadRawresetSampleMetadatarmPeakListRunShinnyAppsetSampleMetadatashowtimeLimitsupdatePtrSetwriteEset

Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitbit64bootbriobroombslibcachemcallrcarcarDatacheckmatechroncliclueclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydescdiffobjdigestdoParalleldplyrDTenviPatevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4magrittrMALDIquantMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminpack.lmminqaMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmenloptrnnetnumDerivopensslpbkrtestpcaMethodspillarpkgbuildpkgconfigpkgloadplotlyplyrpolynompraisepreprocessCoreprocessxpromisesProtGenericspsPSMatchpurrrQFeaturesquantregR6rappdirsRColorBrewerRcppRcppEigenrematch2reshape2rhdf5rhdf5filtersRhdf5librlangrmarkdownrpartrprojrootrstatixrstudioapiS4ArraysS4VectorssassscalesshinyshinyscreenshotsignalsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystestthattibbletidyrtidyselecttinytexUCSC.utilsutf8uuidvctrsviridisviridisLitevsnwaldowithrxfunXMLxtableXVectoryamlzlibbioc

ptairMS: Processing and analysis of PTR-TOF-MS data

Camille Roquencourt, Mélanie Bregou, Paul Zheng, Pierrick Roger and Etienne Thevenot

Rendered fromptairMS.Rmdusingknitr::rmarkdownon Jun 15 2024.

Last update: 2023-10-18
Started: 2021-03-04

Readme and manuals

Help Manual

Help pageTopics
aggregate peakgroup for align functionaggregate
Alignment between samplesalignSamples alignSamples,ptrSet-method
Putative annotation of VOC mz by using the reference compilation from the literatureannotateVOC annotateVOC,data.frame-method annotateVOC,ExpressionSet-method annotateVOC,numeric-method
Calibrates the mass axis with references massescalibration calibration,ptrRaw-method calibration,ptrSet-method
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.changeTimeLimits
Convert a h5 file to mzMLconvert_to_mzML
Creates a ptrSet object form a directorycreatePtrSet
Define the knots locationdefineKnots defineKnots,ptrRaw-method defineKnots,ptrSet-method
Detection and quantification of peaks for a ptrSet object.detectPeak detectPeak,ptrRaw-method detectPeak,ptrSet-method
export sampleMetadataexportSampleMetada
Compute exact mass.formula2mass
get the files directory of a ptrSetgetDirectory
get the file names containing in the directory of a ptrSet or ptrRawgetFileNames getFileNames,ptrRaw-method getFileNames,ptrSet-method
get the peak list of a ptrSet objectgetPeakList
get sampleMetadata of a ptrSetgetSampleMetadata
import a sampleMetadata from a tsv file to a ptrSet objectimportSampleMetadata
Imputes the missing valuesimpute
Impute missing values on an matrix set from an ptrSetimputeMat
Find local maxima with Savitzky Golay filterLocalMaximaSG
Detection and quantification of peaks on a sum spectrum.PeakList PeakList,ptrRaw-method
Plot a ptrSet objectplot,ptrSet,ANY-method plot,ptrSet-method plot.ptrSet
Plot the calibration peaks after calibrationplotCalib plotCalib,ptrRaw-method plotCalib,ptrSet-method
Plot raw average spectrum around a mzRangeplotFeatures plotFeatures,ptrSet-method
Plot method for 'ptrRaw' objectsplotRaw plotRaw,ptrRaw-method plotRaw,ptrSet-method
plot the Total Ion sptectrum (TIC) for one or several files.plotTIC plotTIC,ptrRaw-method plotTIC,ptrSet-method
PTR-TOF-MS raw data from a rhdf5 fileptrRaw-class
A set of PTR-TOF-MS raw data informationsptrSet-class
Read a h5 file of PTR-TOF-MS datareadRaw
reset the default sampleMetadata, containing the suborders names and the acquisition dates as columns.resetSampleMetadata
remove the peakList of an ptrSet objectrmPeakList
Graphical interface of ptairMS workflowRunShinnyApp
set sampleMetadata in a ptrSetsetSampleMetadata
show a ptrRaw objectshow,ptrRaw-method
show a ptrSet objectshow,ptrSet-method
Calculates time limits on the breath tracertimeLimits timeLimits,ptrRaw-method timeLimits,ptrSet-method
update a ptrSet objectupdatePtrSet
Exporting an ExpressionSet instance into 3 tabulated files 'dataMatrix.tsv', sampleMetadata.tsv', and 'variableMetadata.tsv'writeEset writeEset,ExpressionSet-method